Viruses

11 pages, 1517 KiB

Open AccessArticle

A Spatiotemporal Analysis of a High-Resolution Molecular Network Reveals Shifts of HIV-1 Transmission Hotspots in Guangzhou, China

by Huanchang Yan, Yifan Lu, Shunming Li, Hao Wu, Jingyang Hu, Yefei Luo, Qingmei Li, Lingxuan Lai, Weiping Huang, Jing Gu, Lijun Ma, Yuantao Hao, Zhigang Han, Xin-lin Chen and Yu Liu

Viruses 2025, 17(3), 384; https://doi.org/10.3390/v17030384 (registering DOI) - 7 Mar 2025

Abstract

Background: High-resolution and longitudinal HIV molecular surveillance can inform the evolving hotspots to tailor regionally focused control strategies. Methods: HIV-1 pol sequences of three predominant genotypes (CRF01_AE, CRF07_BC, and CRF55_01B) were collected for molecular network reconstruction from people living with HIV (PLWH) in [...] Read more.

Background: High-resolution and longitudinal HIV molecular surveillance can inform the evolving hotspots to tailor regionally focused control strategies. Methods: HIV-1 pol sequences of three predominant genotypes (CRF01_AE, CRF07_BC, and CRF55_01B) were collected for molecular network reconstruction from people living with HIV (PLWH) in Guangzhou (2018–2020). They were categorized by geographical residences into central, suburban, and outer suburban areas. Clustering rates, assortativity coefficients, and intensity matrices were employed to assess transmission dynamics, geographic mixing patterns, and intra- and inter-area transmission, respectively. Results: Of the 2469 PLWH, 55.5% resided in the central area. Clustering rates showed no significant differences across areas (44.5%, 40.6% vs. 45.7%; p = 0.184). However, the transmission hotspots for CRF01_AE and CRF55_01B shifted to the outer suburban area. PLWH tended to form links within their local area (assortativity coefficient = 0.227, p < 0.001), particularly for CRF01_AE (0.512, p < 0.001; intra-area intensity = 69.2%). The central area exhibited the highest but decreasing intra-area transmission (74.5% to 30.2%), while intra- and inter-area transmission involving the outer suburban area increased (23.1% to 38.2%). Conclusions: Despite most PLWH residing in the central area, the outer suburban area emerged as the hotspot, requiring interventions towards both intra- and inter-area transmission. Full article

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

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Characteristics of people living with HIV (PLWH) diagnosed with the three main genotypes in Guangzhou, China (2018–2020). (A) Distribution of PLWH across three areas: central, suburban, and outer suburban. (B) Demographic and social characteristics of PLWH in each area. Full article ">Figure 2
Molecular networks of CRF01_AE, CRF07_BC, and CRF55_01B in Guangzhou, China. Molecular networks were constructed using a pairwise genetic distance threshold of 0.012 substitutions per site. Rows represent the genotypes (CRF01_AE, CRF07_BC, and CRF55_01B) and columns display data for each year (2018, 2019, and 2020). Colors represent different areas of Guangzhou, while shapes indicate infection routes. HET, heterosexual transmission; IDU, injecting drug users; MSM, men who have sex with men. Full article ">Figure 3
Spatiotemporal distribution of people living with HIV (A) and clustering rates (B) in Guangzhou from 2018 to 2020. Maps of PLWH are colored by the proportions of PLWH in a given year, while those of clustering rates are colored by absolute values. Higher values are represented by red hues, whereas lower values are represented in green. Full article ">Figure 4
Spatiotemporal distribution of HIV-1 transmission intensities across different areas of Guangzhou from 2018 to 2020. Colors indicate the proportions of transmission intensity in a given year, with red hues representing higher proportions and green hues representing lower proportions. The color of each grid cell at the intersection of two areas indicates the number of links between the people living with HIV in two areas. Full article ">

16 pages, 664 KiB

Open AccessArticle

Integrating Viral Infection and Correlation Analysis in Passiflora edulis and Surrounding Weeds to Enhance Sustainable Agriculture in Republic of Korea

by Min Kyung Choi

Viruses 2025, 17(3), 383; https://doi.org/10.3390/v17030383 - 7 Mar 2025

Abstract

Passiflora edulis, introduced to the Republic of Korea in 1989 and commercially cultivated since 2012, has faced recent challenges due to viral infections impacting growth, yield, and quality. This study aimed to investigate the viral infections in P. edulis and surrounding weeds [...] Read more.

Passiflora edulis, introduced to the Republic of Korea in 1989 and commercially cultivated since 2012, has faced recent challenges due to viral infections impacting growth, yield, and quality. This study aimed to investigate the viral infections in P. edulis and surrounding weeds at cultivation sites in the Republic of Korea, examining possible correlations between the infections for sustainable agriculture. Over five years, P. edulis and weed samples were collected for virus diagnosis using PCR and RT-PCR assays, analyzing the infection status in both P. edulis and weeds and across weed species/families. The findings revealed infections with EuLCV, PaLCuGdV, CMV, and EAPV in both P. edulis and weeds, with PaLCuGdV showing the highest infection rate. Although no direct correlation was found between the presence of the same viruses in P. edulis and weeds, suggesting that there may be interactions among different viruses, the study highlighted that EuLCV infection could exacerbate symptoms when coinfected by other viruses. The study underscores the importance of implementing preventive measures within greenhouses to control virus transmission, offering insights for strategic management of viral diseases in P. edulis cultivation. These findings support the sustainable production of agricultural products by providing actionable strategies, such as the removal of weeds to eliminate habitats for vectors like whiteflies and aphids and the targeted management of high-incidence weeds from the Asteraceae, Solanaceae, and Oxalidaceae families to prevent and control the spread of EuLCV. Full article

(This article belongs to the Special Issue Biosecurity and Plant Viruses: A Call to Action for a Sustainable Future)

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33 pages, 14092 KiB

Open AccessReview

Vaccines Against Urban Epidemic Arboviruses: The State of the Art

by Cláudio Antônio de Moura Pereira, Renata Pessôa Germano Mendes, Poliana Gomes da Silva, Elton José Ferreira Chaves and Lindomar José Pena

Viruses 2025, 17(3), 382; https://doi.org/10.3390/v17030382 - 6 Mar 2025

Abstract

Arboviruses represent a contemporary global challenge, prompting coordinated efforts from health organizations and governments worldwide. Dengue, chikungunya, and Zika viruses have become endemic in the tropics, resulting in the so-called “triple arbovirus epidemic”. These viruses are transmitted typically through the bites of infected [...] Read more.

Arboviruses represent a contemporary global challenge, prompting coordinated efforts from health organizations and governments worldwide. Dengue, chikungunya, and Zika viruses have become endemic in the tropics, resulting in the so-called “triple arbovirus epidemic”. These viruses are transmitted typically through the bites of infected mosquitoes, especially A. aegypti and A. albopictus. These mosquito species are distributed across all continents and exhibit a high adaptive capacity in diverse environments. When combined with unplanned urbanization, uncontrolled population growth, and international travel—the so-called “triad of the modern world”—the maintenance and spread of these pathogens to new areas are favored. This review provides updated information on vaccine candidates targeting dengue, chikungunya, and Zika viruses. Additionally, we discuss the challenges, perspectives, and issues associated with their successful production, testing, and deployment within the context of public health. Full article

(This article belongs to the Section Animal Viruses)

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17 pages, 745 KiB

Open AccessReview

Epidemiology and Emerging Trends of Zoonotic Viral Diseases of Pigs in India

by Swaraj Rajkhowa, Joyshikh Sonowal, Seema Rani Pegu, Rajib Deb and Vivek Kumar Gupta

Viruses 2025, 17(3), 381; https://doi.org/10.3390/v17030381 - 6 Mar 2025

Abstract

Pigs serve as critical reservoirs and amplifiers for numerous zoonotic viral diseases, presenting substantial public health challenges in India. This study highlights the epidemiology and emerging trends of key zoonotic viruses associated with pigs, emphasizing their role in endemic and emerging disease dynamics. [...] Read more.

Pigs serve as critical reservoirs and amplifiers for numerous zoonotic viral diseases, presenting substantial public health challenges in India. This study highlights the epidemiology and emerging trends of key zoonotic viruses associated with pigs, emphasizing their role in endemic and emerging disease dynamics. Japanese encephalitis virus (JEV) persists as a major concern, with pigs acting as amplifying host, while hepatitis E virus (HEV) remains a prominent cause of viral hepatitis, transmitted via contaminated water and pork products. Emerging high-fatality viral zoonoses caused by Nipah virus (NiV) and recurrent threats from swine influenza virus (SIV) demonstrate that the zoonotic landscape is evolving. Furthermore, zoonotic viruses like rotavirus, pseudorabies (ADV or SuHV-1), porcine astrovirus (PAstV), and Torque teno sus virus (TTSuV) reflect the expanding diversity of pig-associated pathogens in India. Emerging evidence also implicates viruses such as Chandipura virus (CHPV) in localized outbreaks, indicating broader zoonotic potential. Novel risks such as swine acute diarrhea syndrome coronavirus (SADS-CoV) and SARS-CoV-2 emphasize the role of pigs as potential intermediaries for pandemic-prone viruses. This comprehensive study evaluates the prevalence, outbreak dynamics, and public health implications of zoonotic viral diseases of pigs in India, providing valuable direction for developing effective control measures. Full article

(This article belongs to the Special Issue Surveillance, Transmission Dynamics, and Control of Zoonotic Viruses)

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17 pages, 3522 KiB

Open AccessArticle

Differential Responses of Pediatric and Adult Primary Epithelial Cells to Human Metapneumovirus and Respiratory Syncytial Virus Infection

by Pius I. Babawale and Antonieta Guerrero-Plata

Viruses 2025, 17(3), 380; https://doi.org/10.3390/v17030380 - 6 Mar 2025

Abstract

Human metapneumovirus (HMPV) and respiratory syncytial virus (RSV) are pneumoviruses causing lower respiratory tract infections, primarily in infants and children rather than in healthy adults. Human bronchial epithelial cells serve as a viral replication target and source of the innate immune response to [...] Read more.

Human metapneumovirus (HMPV) and respiratory syncytial virus (RSV) are pneumoviruses causing lower respiratory tract infections, primarily in infants and children rather than in healthy adults. Human bronchial epithelial cells serve as a viral replication target and source of the innate immune response to these viruses. To better understand the immune responses induced by RSV and HMPV in the pediatric airway epithelium, we comparatively studied pediatric and adult epithelial responses. We used normal human bronchial epithelial (NHBE) cells cultured in an air–liquid interface culture system (ALI), which helps to mimic the architecture of the human lower respiratory tract epithelium. Our results demonstrate differential viral replication patterns and reduced interferons; and inflammatory cytokines’ expression in pediatric cells compared to adult cells. However, pediatric epithelial cells expressed an increased mucus response and induced a stronger pro-inflammatory response in monocyte-derived dendritic cells. These findings reveal age-dependent immune epithelial responses that may contribute to more severe infections by HMPV and RSV. Full article

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

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Age-related differences in NHBE cell susceptibility to HMPV and RSV infection. NHBE cells from pediatric and adult donors cultured at the air–liquid interface (ALI) and infected with RSV or HMPV. (A) After 7 days of HMPV and RSV infection, cells were stained with H&E staining to assess cell morphology; Scale bar = 50 μm. (B) Kinetics of viral copy numbers. Data represent mean ± SEM from three donors for each age group. Statistical significance was determined using two-way ANOVA with Šídák’s multiple comparisons test (* p < 0.05, ** p < 0.01, *** p < 0.001). Full article ">Figure 2
IFN responses of pediatric and adult NHBE cells to RSV and HMPV infection. NHBE cells were infected with RSV or HMPV. Gene expression of (A) type I IFNs (IFN-α2, IFN-β, IFN-ε, and IFN-ω) and (B) type III IFNs (IFN-λ1 and IFN-λ2/3) was assessed by RT-qPCR at different time points. Statistical significance was determined using two-way ANOVA with Šídák’s multiple comparisons test (* p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001). Non-significant (ns). Full article ">Figure 3
Differential expression of ISGs by pediatric and adult NHBE cells. Adult and pediatric NHBE cells were differentiated in ALI culture and infected with RSV and HMPV. RNA samples were collected at different time points and analyzed for expression of key ISGs (IFIT1, IFIT2, IFIT3, OAS1, MX1, and ISG15) by RT-qPCR. Statistical significance was determined using two-way ANOVA with Šídák’s multiple comparisons test (* p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001). Full article ">Figure 4
Cytokine responses in NHBE cells infected with HMPV or RSV. Adult and pediatric NHBE cells were differentiated in ALI culture and infected with RSV or HMPV. RNA samples were collected at different time points and analyzed by RT-qPCR for the expression of (A) pro-inflammatory cytokines and (B) epithelial alarmins. Statistical significance was determined using two-way ANOVA with Šídák’s multiple comparisons test (* p < 0.05, ** p < 0.01, **** p < 0.0001). Full article ">Figure 5
Cytokine release from human epithelial cells infected with HMPV or RSV. Pediatric and adult NHBE cells were grown in ALI culture and infected with HMPV or RSV. Apical washes were collected at different time points after infection, and concentration of cytokines was determined by LEGENDplex multiplex immunoassay. Statistical significance was determined using two-way ANOVA with Dunnett’s multiple comparisons test (* p < 0.05). Full article ">Figure 6
Mucin expression induced by RSV and HMPV in pediatric and adult NHBE cells. NHBE cells were differentiated in ALI culture and infected with RSV and HMPV. (A) Cells were stained with PAS histological staining on day 7 after infection. Scale bar = 50 μm. (B) Further analysis by RT-qPCR assessed the expression of MUC5AC and MUC5B levels. Statistical significance was determined using two-way ANOVA with Šídák’s multiple comparisons test (** p < 0.01, *** p < 0.001. Non-significant (ns). Full article ">Figure 7
Induction of inflammatory cytokines in mo-DCs co-cultured with either pediatric or adult NHBE cells. mo-DCs were co-cultured with NHBE cells from either pediatric or adult donors infected with HMPV or RSV. (A) Schematic representation of the co-culture setup: Fully differentiated NHBE cells were infected with HMPV or RSV and cultured with mo-DCs for 3 days. mo-DCs were analyzed for the expression of (B) IL-6, (C) TNF-α, and (D) IL-1β by RT-qPCR. Data represent mean ± SEM, n = 4–6. Statistical significance was determined using the Kruskal–Wallis test (* p < 0.05, ** p < 0.01); non-significant (ns). Full article ">

14 pages, 7287 KiB

Open AccessArticle

Genome and Pathogenicity Analysis of an NADC30-like PRRSV Strain in China’s Xinjiang Province

by Honghuan Li, Wei Zhang, Yanjie Qiao, Wenxing Wang, Wenxiang Zhang, Yueli Wang, Jihai Yi, Huan Zhang, Zhongchen Ma and Chuangfu Chen

Viruses 2025, 17(3), 379; https://doi.org/10.3390/v17030379 - 6 Mar 2025

Abstract

The porcine reproductive and respiratory syndrome virus (PRRSV) possesses an inherent ability to adapt to environmental transformations and undergo evolutionary changes, which has imposed significant economic pressure on the global pig industry. Given the potential for recombination among PRRSV genomes and variations in [...] Read more.

The porcine reproductive and respiratory syndrome virus (PRRSV) possesses an inherent ability to adapt to environmental transformations and undergo evolutionary changes, which has imposed significant economic pressure on the global pig industry. Given the potential for recombination among PRRSV genomes and variations in pathogenicity, newly emerging PRRSV isolates are of considerable clinical importance. In this study, we successfully isolated a novel strain named XJ-Z5 from PRRSV-positive samples collected in Xinjiang province in 2022. Through comprehensive genomic sequencing, phylogenetic analysis, and recombination analysis, we confirmed that this strain belongs to the NADC30-like recombinant PRRSV. During pathogenicity tests in piglets, this strain exhibited moderate virulence, causing symptoms such as reduced appetite, persistent fever, and weight loss; however, no mortality cases were observed. Tests conducted at various time points detected the presence of PRRSV nucleic acid in nasal swabs, rectal swabs, tissue samples, and blood, with the highest viral loads found in lung tissue and blood. Serum biochemical tests indicated significant impairment of liver and kidney function. PRRSV antibodies began to appear gradually after 10 days post infection. Hematoxylin and eosin staining revealed substantial pathological changes in lung tissue and lymph nodes. This study enhances our understanding of the epidemiology of PRRSV and underscores the importance of ongoing monitoring and research in light of the challenges posed by the continuous evolution of viral strains. Furthermore, the research emphasizes the urgency of the rapid genomic analysis of emerging viral strains. Through these comprehensive research and monitoring strategies, we aimed to curb the spread of PRRSV more effectively and thus reduce the huge economic losses it caused to the pig industry. Full article

(This article belongs to the Special Issue Research Progress on Porcine Reproductive and Respiratory Syndrome Virus)

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Detection and isolation of PRRSV XJ-Z5 strain. (A) RT-PCR identification of PRRSV NSP2 specific primers; (B) PRRSV XJ-Z5 strain whole-genome segment primer identification map; (C) PRRSV XJ-Z5 strain was inoculated on PAM, Marc-145, NPTr, and MA-104. The area indicated by the red arrow shows cytopathic effect. Full article ">Figure 2
Phylogenetic analysis based on ORF5 and whole-genome. Phylogenetic trees were constructed based on ORF5 (A) and the complete genome (B) of the PRRSV XJ-Z5 strains with 24 representative Chinese reference PRRSV strains. Phylogenetic trees were constructed using the distance-based neighbor-joining method with 1000 bootstrap replicates in MEGA7. The red font highlights the strain PRRSV XJ-Z5 used in this study. Full article ">Figure 3
Recombination analysis. (A) Genomic diagram of the XJ-Z5 strain; (B) the crossover regions in the XJ-Z5 genome were further confirmed by Simplot 3.5.1. The crossover regions identified by Simplot were consistent with the results from the RDP5 analysis (<a href="#viruses-17-00379-t002" class="html-table">Table 2</a>). The y-axis shows the percentage of permutated trees employing a sliding window of 200 nucleotides (nt) and a step size of 30 nt. The other options, including the Kimura (2-parameter) distance model, 2.0 Ts/Tv ratio, neighbor-joining tree model, and 1000 bootstrap replicates were used. Full article ">Figure 4
Pathogenicity results in piglets. (A) Animal challenge test procedure; (B) changes in body temperature after challenge; (C) changes in weight gain after challenge; (D–F) liver and kidney AST, GGT, and CRE biochemical indicators after challenge; (G) the viral load of heart, liver, spleen, lung, and kidney tissues after challenge; (H) the viral load of nasal swabs after challenge; (I) anal swab viral load after challenge; (J) viremia in the blood; (K) a PRRSV-specific antibody level was detected in each group during the challenge study. Full article ">Figure 5
Lung autopsy and pathological sections after challenge infection. (A) Visual changes in lung anatomy; (B) results of lung hematoxylin–eosin staining. Scale bar = 100 µm. (C) Results of lymph node hematoxylin–eosin staining. The arrow indicates the characteristic area of the pathological changes. Scale bar = 100 µm and 20 µm. Full article ">

19 pages, 287 KiB

Open AccessArticle

Estimation of Anti-SARS-CoV-2 IgM/IgG Seroprevalence Among Non-Vaccinated and Vaccinated University Students: A Cross-Sectional Egyptian Study

by Ahmed E. Taha, Ibrahim Amer, Shimaa El Sharawy and Amany A. Ghazy

Viruses 2025, 17(3), 378; https://doi.org/10.3390/v17030378 - 6 Mar 2025

Abstract

It is essential to comprehend the humoral immune response to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and its vaccines to maximize the effectiveness of anti-SARSCoV-2 community immunization efforts. The aim of this cross-sectional study was to determine the seroprevalence of anti-SARS-CoV-2 IgM/IgG among [...] Read more.

It is essential to comprehend the humoral immune response to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and its vaccines to maximize the effectiveness of anti-SARSCoV-2 community immunization efforts. The aim of this cross-sectional study was to determine the seroprevalence of anti-SARS-CoV-2 IgM/IgG among newcomer students at Kafr Elsheikh University in Egypt, whether they had been vaccinated or not. Blood samples from 400 healthy newcomer students (200 non-vaccinated and 200 vaccinated) were evaluated for the presence of anti-SARS-CoV-2 IgM/IgG using colloidal gold immunochromatography lateral flow immunoassay cards, and then the results were confirmed by using specific ELISA tests. The prevalence of anti-SARS-CoV-2 antibodies among the participants (n = 400) was 56.3% for IgG and 13.3% for IgM. Regarding the non-vaccinated participants, 55.0% were females, the mean age was 18.2 years, and the mean BMI was 25.35. Regarding the vaccinated participants, 58.5% were females, the mean age was 18.1 years, and the mean BMI was 25.3. There were statistically non-significant correlations (p ˃ 0.05) between gender, BMI, and each of IgM- or IgG-positivity in both vaccinated and non-vaccinated groups. In total, 41.5% and 48.5% of the anti-SARS-CoV-2 IgM-positive and anti-SARS-CoV-2 IgG-positive participants were non-vaccinated, respectively. Furthermore, 58.5% and 51.5% of the anti-SARS-CoV-2 IgM-positive and anti-SARS-CoV-2 IgG-positive participants were vaccinated, respectively. No statistically significant association (p ˃ 0.05) in immunoglobulins positivity between the anti-SARS-CoV-2 non-vaccinated, and vaccinated groups. The anti-SARS-CoV-2 immunological response of nonsmokers, people who exercise regularly, and those who take vitamin supplements, eat a balanced diet, and use certain herbs is noteworthy. Among the vaccinated subjects, 96.6%, 25.0%, 31.9%, 45.7%, and 7.8% of the IgG-positive group, versus 97.2%, 60.6%, 64.2%, 52.3%, and 6.4% of the IgG-positive non-vaccinated group, were nonsmokers, exercisers, and those taking vitamin supplements, eating a balanced diet, and using herbs, respectively. Furthermore, 93.5%, 32.3%, 35.5%, 48.4%, and 6.5% of the IgM-positive vaccinated group, versus 100.0%, 63.6%, 81.8%, 45.5%, and 4.5% of the IgM-positive non-vaccinated participants, were nonsmokers, physical exercisers, vitamin supplement users, balanced eaters, and herbalists, respectively. Persons who are free from comorbidities, young, non-obese, non-smokers, engage in physical exercise, take vitamins, eat a balanced diet, and use certain immunostimulant herbal supplements, all have a strong anti-SARS-CoV-2 humoral immune response, even if they were not vaccinated. During pandemics, vaccination of this group should not be a priority to preserve vaccine doses for high-risk vulnerable people. Even if there is a lockdown during an anticipated future epidemic or pandemic, we should prioritize healthy eating and lifestyle choices, along with increasing physical activity. Full article

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

15 pages, 1705 KiB

Open AccessArticle

The Genotypes/Subtypes and Antiviral Drug Resistance of the Hepatitis C Virus from Patients in a Tertiary Care Hospital in Nepal

by Hari Prasad Kattel, Sangita Sharma, Kristian Alfsnes, John H.-O. Pettersson, Rahul Pathak, Serina Beate Engebretsen, Komal Raj Rijal, Prakash Ghimire, Åshild K. Andreassen and Megha Raj Banjara

Viruses 2025, 17(3), 377; https://doi.org/10.3390/v17030377 - 6 Mar 2025

Abstract

While direct-acting antivirals (DAAs) are available for the treatment of chronic Hepatitis C virus (HCV) patients in Nepal, knowledge of the circulating genotypes/subtypes and drug target gene mutations of HCV is currently unavailable. Here, we describe HCV genotypes/subtypes and identify antiviral target gene [...] Read more.

While direct-acting antivirals (DAAs) are available for the treatment of chronic Hepatitis C virus (HCV) patients in Nepal, knowledge of the circulating genotypes/subtypes and drug target gene mutations of HCV is currently unavailable. Here, we describe HCV genotypes/subtypes and identify antiviral target gene mutations in patients at a tertiary care hospital using genome data. A cross-sectional study was conducted from December 2019 to February 2024, where PCR followed by whole genome sequencing was performed to identify HCV genotypes/subtypes and drug target gene mutations. Among all the patients who tested positive for anti-HCV, 70.6% (149/211) were HCV RNA positive, while 68.2% (30/44) were genotype/subtype 3a, followed by 1a (18.2%, 8/44) and others (13.6%, 6/44), including new subtypes 3g and 3i from Nepal. Subtype 3a was also the dominant subtype (≥70%) among intravenous drug users and sexual routes of transmission. We found 70.5% of the samples with resistant mutations in the NS3/4A region, 22.7% in NS5A, and 45.5% in NS5B. Resistant mutations against sofosbuvir, pibrentasvir, velpatasvir, daclatasvir, and dasabuvir were found at 25%, 18%, 16%, 16%, and 2%, respectively, mostly on subtype 3a. The predominant HCV genotype/subtype in our patient group was 3a, and resistance mutations against direct-acting antivirals were found in most untreated patients. Full article

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

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16 pages, 4119 KiB

Open AccessArticle

Inhibitory Activity of Hydroxypropyl Methylcellulose on Rhinovirus and Influenza A Virus Infection of Human Nasal Epithelial Cells

by Hsiao-Hui Ong, YongChiat Wong, Jayant Khanolkar, Belinda Paine, Daniel Wood, Jing Liu, Mark Thong, Vincent T. Chow and De-Yun Wang

Viruses 2025, 17(3), 376; https://doi.org/10.3390/v17030376 - 6 Mar 2025

Abstract

The nasal epithelium is the primary site for entry of respiratory viruses. In comparison to oral administration, nasal drug applications directed locally to the site of infection can serve as early interventional barriers against respiratory virus pathogenesis by limiting viral spread in the [...] Read more.

The nasal epithelium is the primary site for entry of respiratory viruses. In comparison to oral administration, nasal drug applications directed locally to the site of infection can serve as early interventional barriers against respiratory virus pathogenesis by limiting viral spread in the upper airway. Experiments on the diffusion of methylene blue and nanoparticles in both water and low pH conditions revealed that hydroxypropyl methylcellulose (HPMC) can act as an effective physical barrier. This study also evaluated the activity of HPMC as a barrier against common respiratory viruses, i.e., rhinovirus (RV) and influenza A virus (IAV) using the in vitro human nasal epithelial cell (hNEC) model. Utilizing the hNEC infection model, we assessed the protective effects of HPMC in pH 3.5 and pH 7 buffers against RV and IAV. Acidic and pH-neutral buffers and HPMC dissolved in acidic and pH-neutral buffers were administered for 4 h prior to virus infection and at 4 h post-infection (hpi). The apical supernatant was harvested at 24 hpi to determine the viral loads of RV and IAV (H1N1 and H3N2). HPMC was demonstrated to exert protective effects in the infected hNECs independent of acidic pH. Pre-treatment with HPMC in acidic buffer significantly diminished viral loads for both RV and IAV infections of hNECs. Similarly, direct treatment of HPMC in acidic buffer after infection (4 hpi) also effectively decreased viral loads of both RV and IAV. Moreover, treatment using HPMC in acidic buffer before or after infection did not affect the epithelial integrity and ciliary function of hNECs. This study demonstrates the protective effects of HPMC in acidic buffer against RV and IAV infections of the human nasal epithelium. Full article

(This article belongs to the Special Issue Pharmacology of Antiviral Drugs)

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10 pages, 779 KiB

Open AccessArticle

Pandemic-Driven Shifts in Epstein-Barr Virus (EBV) Epidemiology: Single Center Study

by Maria Eugenia Amarillo, Karen Lindl, Mercedes García Lombardi, Maria Victoria Preciado, Elena De Matteo and Paola Chabay

Viruses 2025, 17(3), 375; https://doi.org/10.3390/v17030375 - 6 Mar 2025

Abstract

Social distancing, hand hygiene, mask wearing, surface decontamination, travel restrictions, and school closures have been implemented worldwide to control coronavirus disease 2019 (COVID-19). It was reported that the number of EBV infections as well as the age characteristics of infected persons before and [...] Read more.

Social distancing, hand hygiene, mask wearing, surface decontamination, travel restrictions, and school closures have been implemented worldwide to control coronavirus disease 2019 (COVID-19). It was reported that the number of EBV infections as well as the age characteristics of infected persons before and after the COVID-19 pandemic significantly decreased in children from China. Since no studies have explored the changes in EBV-associated lymphomas so far, our aim was to explore EBV infection and viral-associated Hodgkin lymphoma (HL) in a pediatric cohort from a single center. A decrease in EBV+ children by serology was proved, in particular, in those undergoing primary infection, along with a significant increase in the mean age of healthy carriers. Furthermore, a decrease in EBV-associated pediatric cHL was observed post-pandemic, particularly in the NS subtype, with a marked decrease in cases diagnosed from 2022 onward. Even though the underlying reasons for the change in incidence rates seen in this study still remain speculative, it could be hypothesized that, after the pandemic, older children have a better ability to control the EBV-mediated lymphomagenesis, based on the fact that the age of infected patients increased. Full article

(This article belongs to the Special Issue EBV and Disease: New Perspectives in the Post COVID-19 Era)

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18 pages, 4349 KiB

Open AccessArticle

Co-Infection Dynamics of Baculovirus Penaei (BP–PvSNPV) in Penaeus vannamei Across Latin America

by Pablo Intriago, Bolivar Montiel, Mauricio Valarezo, Nicole Cercado, Alejandra Montenegro, María Mercedes Vásquez, Melany del Barco and Yamilis Cataño

Viruses 2025, 17(3), 374; https://doi.org/10.3390/v17030374 - 5 Mar 2025

Abstract

Baculovirus penaei (BP) is an enteric virus infecting the hepatopancreas and anterior midgut of shrimp, particularly affecting early developmental stages and contributing to hatchery losses. While BP’s role in co-infections is increasingly recognized, its impact on later life stages remains unclear. Despite advancements [...] Read more.

Baculovirus penaei (BP) is an enteric virus infecting the hepatopancreas and anterior midgut of shrimp, particularly affecting early developmental stages and contributing to hatchery losses. While BP’s role in co-infections is increasingly recognized, its impact on later life stages remains unclear. Despite advancements in molecular diagnostics, its high genetic diversity complicates reliable detection, often leading to discrepancies between PCR results and histological observations of occlusion bodies. This study evaluated seven primer pairs for BP detection in Penaeus vannamei. Among histologically confirmed cases, only 6% tested positive with the BPA/BPF primer and 3% with BPA/BPB, while the remaining primers failed to amplify BP, highlighting significant diagnostic limitations. Histopathology revealed bacterial co-infections alongside BP, with advanced cases showing intranuclear occlusion bodies, hepatopancreatic necrosis, and epithelial detachment. These findings underscore the urgent need for improved molecular diagnostics to accurately assess BP prevalence, its role in co-infections, and its overall impact on shrimp health in Latin America. Further research is essential to refine detection methods and determine BP’s pathogenic significance beyond early developmental stages. Full article

(This article belongs to the Special Issue Viruses in Mass-Reared Invertebrates, 2nd Edition)

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17 pages, 9975 KiB

Open AccessArticle

Oropouche Virus: Isolation and Ultrastructural Characterization from a Human Case Sample from Rio de Janeiro, Brazil, Using an In Vitro System

by Ana Luisa Teixeira de Almeida, Igor Pinto Silva da Costa, Maycon Douglas do Nascimento Garcia, Marcos Alexandre Nunes da Silva, Yasmim Gonçalves Lazzaro, Ana Maria Bispo de Filippis, Fernanda de Bruycker Nogueira and Debora Ferreira Barreto-Vieira

Viruses 2025, 17(3), 373; https://doi.org/10.3390/v17030373 - 5 Mar 2025

Abstract

The Oropouche virus (OROV) is a segmented negative-sense RNA arbovirus member of the Peribunyaviridae family, associated with recurring epidemics of Oropouche fever in Central and South America. Since its identification in 1955, OROV has been responsible for outbreaks in both rural and urban [...] Read more.

The Oropouche virus (OROV) is a segmented negative-sense RNA arbovirus member of the Peribunyaviridae family, associated with recurring epidemics of Oropouche fever in Central and South America. Since its identification in 1955, OROV has been responsible for outbreaks in both rural and urban areas, with transmission involving sylvatic and urban cycles. This study focuses on the characterization of an OROV isolate from a human clinical sample collected in the state of Rio de Janeiro, a non-endemic region in Brazil, highlighting ultrastructural and morphological aspects of the viral replicative cycle in Vero cells. OROV was isolated in Vero cell monolayers which, following viral inoculation, exhibited marked cytopathic effects (CPEs), mainly represented by changes in cell morphology, including membrane protrusions and vacuolization, as well as cell death. Studies by transmission electron microscopy (TEM) revealed significant ultrastructural changes, such as apoptosis, intense remodeling of membrane-bound organelles and signs of rough endoplasmic reticulum and mitochondrial stress. Additionally, the formation of specialized cytoplasmic vacuoles and intra- and extracellular vesicles emphasized trafficking and intercellular communication as essential mechanisms in OROV infection. RT-qPCR studies confirmed the production of viral progeny in high titers, corroborating the efficiency of this experimental model. These findings contribute to a better understanding of the cytopathogenic mechanisms of OROV infection and the contribution of cellular alterations in OROV morphogenesis. Full article

(This article belongs to the Special Issue Oropouche Virus (OROV): An Emerging Peribunyavirus (Bunyavirus))

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Monolayers of Vero cells in control conditions and infected with Oropouche virus (OROV) at 48, 72, and 96 h post-infection (h p.i.). Bright-field microscopy analysis revealed conformational changes in the membrane as the infection progresses, including the formation of projections and membrane partitioning (insets), which are indicative of apoptosis. Full article ">Figure 2
Cytopathic effects in Vero cells infected with Oropouche virus—cellular response and damage. (A) Uninfected Vero cell. Membrane blebbing (MB). (B–F) OROV-infected cells. (B) Apoptotic bodies (AB), cytoplasmic vacuoles (CV), mitochondrial clustering (MC). (C) Filopodia formation (FF), mitochondrial clustering (MC). (D) Apoptotic bodies (AB), pyknotic nucleus (PN). (E) Mitochondrial cristae disorganization (CD), hypercondensation of chromatin (HC). (F) Lipid droplets (LD), mitochondrial clustering (MC), myelin figure (MF), multilamellar bodies (ML). Full article ">Figure 3
Cytopathic effects in Vero cells infected with Oropouche virus—membrane remodeling. (A) Cytoplasmic vacuoles (CV), plasma membrane blebbing (MB), mitochondrial clustering (MC), nuclear membrane invagination (NI). (B) Multilamellar body (ML), multivesicular body (MVB), rough endoplasmic reticulum (RER) thickening (RT). (C) Autophagy components (AC), budding vesicles (BV). (D) Budding vesicles (BV), RER cisterns (RC). (E) Budding vesicles (BV), filopodia formation (FF), RER cisterns (RC). (F) Lipid droplet (LD), multivesicular cargo (MV), RER cisterns (RC). (G) Multivesicular cargo (MV), RER thickening (RT). Full article ">Figure 4
Cytopathic effects in Vero cells infected with Oropouche virus—rough endoplasmic reticulum (RER) and mitochondrial stress. (A) Mitophagy (MA), mitochondrial swelling (MS), RER thickening (RT). (B) Cytoplasmic vacuole (CV), mitochondrial swelling (MS), pyknotic nucleus (PN), RER cisterns (RC), RER thickening (RT). (C) Myelin figures (MF), mitochondrial swelling (MS), vacuolar degeneration of mitochondria (VD). (D) Mitochondrial swelling (MS), vacuolar degeneration of mitochondria (VD). (E) Cytoplasmic vacuole (CV), giant mitochondria (GM), lipid droplets (LD), multilamellar bodies (ML). Full article ">Figure 5
Cytopathic effects in Vero cells infected with Oropouche virus—viral replication insights. (A,B) Multivesicular body (MVB), viral particles (VP). (A) Immature viral particles (IP), intraluminal vesicle (IV). (B–D) Clathrin-coated vesicles (CCV). (B) Apoptotic body (AB). (C) Intraluminal vesicle (IV), multivesicular body (MVB). (D) Filopodia formation (FF). (E,F) Viral particles (VP). (E) Multivesicular body (MVB), myelin figures (MF). (F) Mitochondrial swelling (MS). Full article ">Figure 6
Morphology of Oropouche viral particles. (A) Viral particle (arrowhead) in extracellular space, adsorbed to the membrane surface. (B–F) Viral particles (arrowhead) into cytoplasm. (C–E) Morphological diversity noted within multivesicular bodies, showcasing particles at different stages of morphogenesis (arrowhead), leading to variations in size and electron density. (C) Reduced diameter observed in indicated particles (arrowhead) reflects incomplete particles. (F) Additional location of viral particles (arrowhead) within cytoplasm, associated with Golgi apparatus stacks. Inset: (C,D) <a href="#viruses-17-00373-f005" class="html-fig">Figure 5</a>A. (E) <a href="#viruses-17-00373-f005" class="html-fig">Figure 5</a>E. (F) <a href="#viruses-17-00373-f005" class="html-fig">Figure 5</a>F. All particles exhibited a spherical shape, with variation in diameter indirectly reflecting maturation status of these particles. Full article ">Figure 7
Morphometric analysis of the mitochondria. (A) Micrograph of the uninfected cell. (B) Micrograph of the OROV-infected cell culture to illustrate morphometric procedure. All mitochondria were counted, excluding those that were not fully within the field (black arrow). For the mitochondrial density of each micrography, the evaluated areas (yellow rectangle) were defined as the boundary surrounding the outermost mitochondria (yellow crosses). The cross-sectional area (black dashed line) and minor and major axes (continuous and dashed white line, respectively) were measured in all mitochondria (C) Mitochondrial density of 20 micrographs per group. Median: 0.29 mitochondria/μm2 (95% CI, 0.25–0.31)—control group), and 1.78 mitochondria/μm2 (95% CI, 1.27–2.3)—OROV-infected group. The data presented in panels (C,D) correspond to the micrographs totaling 500 mitochondria per group (control and OROV-infected). (D) Mitochondrial cross-sectional area. Median: 0.37 μm2 (95% CI, 0.32–0.36)—control group, and 0.08 μm2 (95% CI, 0.07–0.08)—OROV-infected group. **** p < 0.0001—Mann–Whitney test. (E) Distribution of the frequencies of mitochondrial circularity index. The y-axis indicates the number of mitochondria located within the circularity index range specified by the center bins on the x-axis. Median: 0.72—control group, and 0.68—OROV-infected group. Full article ">

15 pages, 1736 KiB

Open AccessReview

Emerging Roles of m7G-Cap Hypermethylation and Nuclear Cap-Binding Proteins in Bypassing Suppression of eIF4E-Dependent Translation

by Kathleen Boris-Lawrie, Jessica Liebau, Abdullgadir Hayir and Xiao Heng

Viruses 2025, 17(3), 372; https://doi.org/10.3390/v17030372 - 5 Mar 2025

Abstract

Translation regulation is essential to the survival of hosts. Most translation initiation falls under the control of the mTOR pathway, which regulates protein production from mono-methyl-guanosine (m7G) cap mRNAs. However, mTOR does not regulate all translation; hosts and viruses alike employ alternative pathways, [...] Read more.

Translation regulation is essential to the survival of hosts. Most translation initiation falls under the control of the mTOR pathway, which regulates protein production from mono-methyl-guanosine (m7G) cap mRNAs. However, mTOR does not regulate all translation; hosts and viruses alike employ alternative pathways, protein factors, and internal ribosome entry sites to bypass mTOR. Trimethylguanosine (TMG)-caps arise from hypermethylation of pre-existing m7G-caps by the enzyme TGS1 and are modifications known for snoRNA, snRNA, and telomerase RNA. New findings originating from HIV-1 research reveal that TMG-caps are present on mRNA and license translation via an mTOR-independent pathway. Research has identified TMG-capping of selenoprotein mRNAs, junD, TGS1, DHX9, and retroviral transcripts. TMG-mediated translation may be a missing piece for understanding protein synthesis in cells with little mTOR activity, including HIV-infected resting T cells and nonproliferating cancer cells. Viruses display a nuanced interface with mTOR and have developed strategies that take advantage of the delicate interplay between these translation pathways. This review covers the current knowledge of the TMG-translation pathway. We discuss the intimate relationship between metabolism and translation and explore how this is exploited by HIV-1 in the context of CD4+ T cells. We postulate that co-opting both translation pathways provides a winning strategy for HIV-1 to dictate the sequential synthesis of its proteins and balance viral production with host cell survival. Full article

(This article belongs to the Special Issue Viral Strategies and Cellular Countermeasures that Regulate mRNA Access to the Translation Apparatus)

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18 pages, 5404 KiB

Open AccessArticle

Evolutionary Studies on the Coxsackievirus A-24 Variants Causing Acute Hemorrhagic Conjunctivitis with Emphasis on the Recent Outbreak of 2023 in India

by Sanjaykumar Tikute, Jahnabee Boro, Vikas Sharma, Anita Shete, Alfia Fathima Ashraf, Ranjana Mariyam Raju, Sarah Cherian and Mallika Lavania

Viruses 2025, 17(3), 371; https://doi.org/10.3390/v17030371 - 5 Mar 2025

Abstract

Acute Hemorrhagic Conjunctivitis (AHC) is primarily caused by viral infections, with Coxsackievirus A-24v (CV-A24v) being a significant culprit. Enteroviruses, including CV-A24v, are responsible for global AHC outbreaks. Over time, CV-A24v has evolved, and genotype IV (GIV) has become the dominant strain. This study [...] Read more.

Acute Hemorrhagic Conjunctivitis (AHC) is primarily caused by viral infections, with Coxsackievirus A-24v (CV-A24v) being a significant culprit. Enteroviruses, including CV-A24v, are responsible for global AHC outbreaks. Over time, CV-A24v has evolved, and genotype IV (GIV) has become the dominant strain. This study focused on examining the genetic features and evolutionary trends of CV-A24v responsible for the recent AHC outbreak of 2023 in India. Researchers isolated viral strains from ocular swabs and confirmed the presence of CV-A24v using reverse transcriptase quantitative PCR (RT-qPCR) and whole-genome sequencing. Genomic comparisons between isolates of 2023 and those from a previous outbreak in 2009 were conducted. Phylogenetic analysis revealed that the 2023 isolates formed a distinct cluster within GIV-5 and were related to recent strains from China and Pakistan. The older Indian isolates from 2009 grouped with GIV-3. New subclades, GIV-6 and GIV-7, were also identified in this study, indicating the diversification of CV-A24. Molecular clock and phylogeographic analysis traced the virus’s circulation back to the 1960s, with the common ancestor likely to have originated in Singapore in 1968. The 2023 Indian strains probably originated from Thailand around 2014, with subsequent spread to China and Pakistan. This study concluded that the 2023 outbreak was caused by a genetically distinct CV-A24v strain with nine mutations, underlining the virus’s ongoing evolution and adaptations and offering valuable insights for future outbreak control. Full article

(This article belongs to the Special Issue Coxsackieviruses, Polioviruses and Associated Diseases (Second Edition))

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Symptomatic profile of the patients whose samples were selected for virus isolation. Full article ">Figure 2
Schematic representation of the workflow. Full article ">Figure 3
Isolation of CV-A24v in Hela cell line: (A) appearance of normal HeLa Cell line; (B) HeLa cell line showing 80% CPEs on day 5 post-inoculation. Full article ">Figure 4
Maximum likelihood phylogenetic analysis based on 171 VP1 sequences of CV-A24v. The tree tips are color-coded according to the countries of origin for the CV-A24v viral isolates. Indian isolates from 2009 and 2023 are highlighted with red circles. Information regarding the CV-A24v genotype is displayed in a grey vertical bar, while the sub-genotype is indicated with a red vertical bar positioned in front of the phylogenetic tree. Full article ">Figure 5
Maximum likelihood phylogenetic analysis based on 84 whole-genome CV-A24v sequences. The tree tips are color-coded according to the countries of origin for the CV-A24v viral isolates. Indian isolates from 2009 and 2023 are highlighted with red circles. Information regarding the CV-A24v genotype is displayed in a grey vertical bar, while the sub-genotype is indicated with a red vertical bar positioned in front of the phylogenetic tree. Full article ">Figure 6
Maximum likelihood phylogenetic analysis based on 92 VP2 sequences of CV-A24v. The tree tips are color-coded according to the countries of origin for the CV-A24v isolates. Indian isolates from 2009 and 2023 are highlighted with red circles. Information regarding the CV-A24v genotype is displayed in a grey vertical bar, while the sub-genotype is indicated with a red vertical bar positioned in front of the phylogenetic tree. Full article ">Figure 7
MCC phylogenetic analysis based on 171 VP1 sequences of CV-A24v. The branches and tips of the tree are color-coded according to the countries of origin for the CV-A24v isolates. Indian viral isolates from 2009 and 2023 are highlighted with red circles. Information regarding the CV-A24v genotype is displayed in a grey vertical bar, while the sub-genotype is indicated with a red vertical bar positioned in front of the phylogenetic tree. The node labels are according to country posterior probability and ancestral states. TMRCAs values at 95% HPDs are indicated with bars at nodes of the tree. Full article ">Figure 8
Geographic distribution and transition rates of CV-A24v isolates between countries, with supported posterior probabilities greater than 0.5. The figure represents the transmission routes using SPREAD software v0.9.7.1 using the world map [<a href="#B22-viruses-17-00371" class="html-bibr">22</a>]. Lines between countries indicate the possible transmission routes of CV-A24v. Colored lines indicate BF values and the posterior probability. Full article ">

12 pages, 1721 KiB

Open AccessArticle

A Novel Multi-Gene Combined RT-PCR Assay for Rapid and Sensitive Detection of Maize Dwarf Mosaic Virus

by Yujie Jin, Xihong Chen, Min Li, Xiaoqi Zhang, Wei Cai, Jianguo Shen, Yongjiang Zhang and Fangluan Gao

Viruses 2025, 17(3), 370; https://doi.org/10.3390/v17030370 - 5 Mar 2025

Abstract

Maize, a staple food and cash crop worldwide, also serves as a critical industrial raw material. However, it is significantly threatened by viral pathogens, particularly maize dwarf mosaic virus (MDMV), the primary cause of maize dwarf mosaic disease, a debilitating condition affecting maize [...] Read more.

Maize, a staple food and cash crop worldwide, also serves as a critical industrial raw material. However, it is significantly threatened by viral pathogens, particularly maize dwarf mosaic virus (MDMV), the primary cause of maize dwarf mosaic disease, a debilitating condition affecting maize cultivation. This study aims to establish a multi-gene combined RT-PCR assay for the rapid specific, sensitive, and reliable detection of MDMV without the need for special expensive equipment. Samples of imported maize, sorghum, and barley were collected from ports in Fujian and Shanghai. Primers targeting the coat protein (CP) and cytoplasmic inclusion protein (CI) genes of MDMV were designed and optimized. Through the design and screening of primers, as well as the optimization of reaction conditions and primer concentrations, a multi-gene combined RT-PCR assay was established to simultaneously detect both genes. Additionally, a real-time fluorescent-based RT-PCR (RT-qPCR) assay was developed using the CP gene to confirm the accuracy of multi-gene combined RT-PCR assay. The sensitivity of the optimized multi-gene combined RT-PCR assay enables the detection of MDMV in infected maize leaf crude extracts at dilutions of 5.37 pg/μL. This assay exhibited excellent specificity, high sensitivity, and robust repeatability, providing swift and accurate detection of MDMV. The multi-gene combined RT-PCR assay offers precise and efficient technical support for MDMV detection and contributes to improved maize production practices. Full article

(This article belongs to the Special Issue Plant Viruses and Their Vectors: Epidemiology and Control)

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34 pages, 42914 KiB

Open AccessArticle

Pseudomonas Phage Lydia and the Evolution of the Mesyanzhinovviridae Family

by Konstantin Troshin, Nina Sykilinda, Sofia Shuraleva, Anna Tokmakova, Nikolay Tkachenko, Lidia Kurochkina, Konstantin Miroshnikov, Natalia Suzina, Ekaterina Brzhozovskaya, Kristina Petrova, Stepan Toshchakov and Peter Evseev

Viruses 2025, 17(3), 369; https://doi.org/10.3390/v17030369 - 4 Mar 2025

Abstract

Phage Lydia, a newly isolated siphovirus infecting Pseudomonas aeruginosa, was characterized with respect to its basic kinetic properties and subjected to comparative bioinformatic analysis with related phages. The phage exhibited a restricted host range, with lytic activity observed against 7 of 30 [...] Read more.

Phage Lydia, a newly isolated siphovirus infecting Pseudomonas aeruginosa, was characterized with respect to its basic kinetic properties and subjected to comparative bioinformatic analysis with related phages. The phage exhibited a restricted host range, with lytic activity observed against 7 of 30 tested isolates. The genome of phage Lydia consists of a 61,986 bp dsDNA molecule and contains 89 predicted genes. Bioinformatic analysis suggests the presence of a DNA modification system, but no apparent genes associated with lysogeny or antibiotic resistance were identified. Taxonomic classification places Lydia within the Mesyanzhinovviridae family, Rabinowitzvirinae subfamily, and Yuavirus genus, with the closest relation to Pseudomonas virus M6. Comprehensive bioinformatic studies, including structural modelling and analysis of phage proteins, as well as comparative taxonomic, phylogenomic, and pangenomic analyses of the Mesyanzhinovviridae family, revealed relationships between proteins of Mesyanzhinovviridae phages, proteins from other phage groups, encapsulins, and a gene transfer agent (GTA) particle from Rhodobacter capsulatus. These analyses uncovered patterns of evolutionary history within the family, characterized by genetic exchange events alongside the maintenance of a common genomic architecture, leading to the emergence of new groups within the family. Full article

(This article belongs to the Section Bacterial Viruses)

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6 pages, 1083 KiB

Open AccessCase Report

Amoxicillin-Induced Atypical Exanthema in a Patient with EBV-Related Nasopharyngeal Carcinoma: A Case Report

by Matteo Carpani, Davide Smussi, Andrea Esposito, Francesca Consoli, Alfredo Berruti and Andrea Alberti

Viruses 2025, 17(3), 368; https://doi.org/10.3390/v17030368 - 4 Mar 2025

Abstract

Introduction: The concomitant use of antibiotics, especially beta lactams, during acute EBV infection is widely associated with an increased risk of skin manifestations; the actual pathophysiology and prevalence of this phenomenon are still debated. Case report: We present the first reported case of [...] Read more.

Introduction: The concomitant use of antibiotics, especially beta lactams, during acute EBV infection is widely associated with an increased risk of skin manifestations; the actual pathophysiology and prevalence of this phenomenon are still debated. Case report: We present the first reported case of atypical exanthema associated with amoxicillin intake in a patient with EBV-related nasopharyngeal carcinoma. We recorded a pattern in the plasma EBV-DNA load consisting of a significant increase at the onset of the rash with a sudden remission after its resolution. The patient recovered without sequelae. Discussion/Conclusions: The temporal relationship and the reported data on rash morphology, clinical findings and triggering factors support a possible correlation between the intake of beta-lactam antibiotics, particularly amoxicillin, and the onset of cutaneous manifestations in a patient with nasopharyngeal carcinoma. Such reactions can be a challenging differential diagnosis and may warrant increased provider consideration when choosing to prescribe beta lactams in patients affected by nasopharyngeal cancer. Full article

(This article belongs to the Special Issue EBV and Disease: New Perspectives in the Post COVID-19 Era)

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14 pages, 233 KiB

Open AccessReview

Relationship Between Human Papilloma Virus and Upper Gastrointestinal Cancers

by Ömer Vefik Özozan, Hikmet Pehlevan-Özel, Veli Vural and Tolga Dinç

Viruses 2025, 17(3), 367; https://doi.org/10.3390/v17030367 - 4 Mar 2025

Abstract

The human papillomavirus (HPV) is an oncogenic DNA virus that is the most commonly transmitted sexually transmitted virus. There is substantial evidence that HPV is associated with different types of cancer. While the majority of studies have concentrated on urogenital system cancers and [...] Read more.

The human papillomavirus (HPV) is an oncogenic DNA virus that is the most commonly transmitted sexually transmitted virus. There is substantial evidence that HPV is associated with different types of cancer. While the majority of studies have concentrated on urogenital system cancers and head and neck cancers, the relationship between HPV and gastrointestinal system cancers, particularly esophageal cancers, has also been the subject of investigation. Given that HPV is a disease that can be prevented through vaccination and treated with antiviral agents, identifying the types of cancers associated with the pathogen may inform the treatment of these cancers. This comprehensive review examines the relationship between HPV and cancers of the upper gastrointestinal tract, highlighting the oncogenic mechanisms of the virus and its reported prevalence. A deeper understanding of HPV’s association with cancer is relevant to the further development of cancer therapies. Full article

(This article belongs to the Special Issue Papillomavirus-Induced Oncogenesis: Current Insights and Future Directions)

23 pages, 1120 KiB

Open AccessReview

Acute HIV-1 Infection: Paradigm and Singularity

by Antoine Chéret

Viruses 2025, 17(3), 366; https://doi.org/10.3390/v17030366 - 3 Mar 2025

Abstract

Acute HIV-1 infection (AHI) is a transient period where the virus causes evident damage to the immune system, including an extensive apoptosis of CD4+ T cells associated with a high level of activation and a major cytokine storm to fight the invading virus. [...] Read more.

Acute HIV-1 infection (AHI) is a transient period where the virus causes evident damage to the immune system, including an extensive apoptosis of CD4+ T cells associated with a high level of activation and a major cytokine storm to fight the invading virus. HIV infection establishes persistence by integrating the viral genome into host cell DNA in both replicating and non-replicating forms, effectively hiding from immune surveillance within infected lymphocytes as cellular reservoirs. The measurement of total HIV-1 DNA in peripheral blood mononuclear cells (PBMCs) is a reliable reflection of this reservoir. Initiating treatments during AHI with nucleoside reverse transcriptase inhibitors (NRTIs) and/or integrase strand transfer inhibitors (INSTIs) is essential to alter the dynamics of the global reservoir expansion, and to reduce the establishment of long-lived cellular and tissue reservoirs, while preserving and enhancing specific and non-specific immune responses. Furthermore, some of the patients treated at the AHI stage may become post-treatment controllers and should be informative regarding the mechanism of viral control, so patients treated during AHI are undoubtedly the best candidates to test innovative remission strategies toward a functional cure that could play a pivotal role in long-term HIV control. AHI is characterized by high levels of viral replication, with a significant increase in the risk of HIV transmission. Detecting AHI and initiating early treatment following diagnosis provides a window of opportunity to control the epidemic, particularly in high-risk populations. Full article

(This article belongs to the Special Issue Acute HIV Infections)

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Patho-physiological model of acute and recent HIV infection. Acute HIV infection marks the onset of a virological and immune storm at its peak. The initial viral replication in infected productive cells leads to a high production of virions and viral proteins, which triggers first intense innate immunity response (including myeloid cells) and contribute to the immune storm by inducing activation and inflammation, with the production of inflammatory cytokines and chemokines, and mobilizing cellular and immune responses. Acute infection elicits intense immune responses, characterized by massive T cell activation and proliferation, which facilitate cell infection and the establishment of a comprehensive HIV reservoir. This reservoir includes both latently infected and productive cells within lymph nodes and tissues. A more or less attenuated level of inflammation and various immune stimulations then persist, maintaining a continuous model with constant viral replication in the absence of treatment. Full article ">Figure 2
Development of Biological Markers at the time of Acute and recent HIV Infection: The progression of HIV-1 infection can be divided into six distinct stages named Fiebig stages based on results of standard laboratory tests. They are characterized by the sequential detection starting with HIV-1 RNA, p24 antigen and specific antibodies against HIV-1 proteins, detected by Elisa (the 4th generation, the more sensitive), including anti-p34, detected by Western blot analysis. In the very first step of acute HIV infection, the pattern of the Western blot may be indeterminate, then weak or with an isolated anti-p24 band, followed by reactivity against gp41 and progressing to a complete pattern. HIV viral reservoir can be estimated using the quantification of total HIV-DNA in PBMC, which is detectable in the first step. For newborns, the diagnosis of acute HIV infection can be established by quantifying plasma HIV-RNA in the first days of life, as well as by measuring total blood HIV-DNA. A plus sign indicates a positive test result, a minus sign denotes a negative result, and a plus-minus sign represents a borderline-positive result. Adapted from Cohen et al, NEJM, 2011 [<a href="#B19-viruses-17-00366" class="html-bibr">19</a>]. Full article ">

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