Search Results (1,771)

Hepatitis B virus (HBV) pregenomic RNA (pgRNA), transcribed directly from nuclear covalently closed circular DNA (cccDNA), is an essential component in viral replication. The synthesis and encapsidation of pgRNA depend significantly on the transcriptional activity of cccDNA, making serum pgRNA a recently recognized non-invasive biomarker for evaluating cccDNA activity. However, its clinical application is limited by factors including preanalytical variables, methodological inconsistencies in detection, and a lack of standardization in quantification. This review provides an overview of the biological origins of pgRNA and its critical role in the HBV replication cycle, highlighting the stability challenges encountered during the collection, processing, and storage of plasma/serum samples. Furthermore, it analyzes recent significant advancements in pgRNA detection technologies, encompassing modified reverse transcription quantitative polymerase chain reaction (RT-qPCR), nucleocapsid-captured methodologies, automated testing platforms, multiplex digital PCR, isothermal amplification, and clustered regularly interspaced short palindromic repeats-based assays. A comparison of these technologies revealed that discrepancies in pgRNA quantification arise primarily from variations in sample processing and measurement systems, rather than from inherent biological limitations. Therefore, establishing standardized sample handling procedures, harmonized detection methods, and unified measurement systems is imperative before pgRNA can be reliably applied to monitor treatment, guide cessation decisions, or evaluate cure in chronic hepatitis B. Full article

Infectious bronchitis virus (IBV) causes a highly contagious disease in chickens. The prevalence of GVI-1 is increasing; however, the genomic characteristics and antigenic properties of this genotype strain remain insufficiently characterized. In this study, the genome characteristics and antigenic properties of a naturally attenuated CK/CH/SC/YC_GVI-1-DK/LMB20210104 (abbreviated as YC_GVI-1) strain were systematically analyzed. YC_GVI-1 occupies a distinct phylogenetic lineage and shares a similarity of 98.2%, the highest nucleotide sequence homology, with the reference strain CK/CH/FJ/202005 (accession number: MW791835.1). This strain was likely originated through a genetic recombination event between two major parental strains, CK/CH/FJ/202005 and CK/CH/GX/HX (accession number: PP817796.1). However, its S protein harbors ten unique amino acid substitutions, compared to the same protein in the other two virulent strains in the same genotype. AlphaFold3-based structural prediction reveals that one of these substitutions, methionine 485 to valine substitution, may induce a conformational change in the adjacent phenylalanine residue at position 431, resulting in a shift in the local secondary structure from β-sheet to random coil. Characterization of its antigenicity showed that this strain induces a strong humoral immune response, with neutralizing antibody titers of 2^6.40 against homologous strain YC_GVI-1 and 2^4.00 against heterologous strain JS96_GI-19. Furthermore, vaccination of chickens with this strain conferred complete protection (100%) against JS96_GI-19. The findings provide novel insights into the molecular evolution and antigenicity of YC_GVI-1, offering key information for improving IBV surveillance and vaccine development. Full article

Parvovirus B19 is a DNA virus. Most parvoviruses infect animals; Parvovirus B19 infects humans. Parvovirus B19 is mainly transmitted through respiratory droplets during close contact, but additional routes such as transmission through contaminated blood products and vertical transmission from mother to fetus have also been documented. Infections occur throughout the year, with a seasonal increase between late winter and early summer. Clinical symptoms depend on age, and on patients’ immune status. Healthy, immunocompetent individuals experience asymptomatic or mild infections including a febrile rash; serious complications rarely appear, such as rheumatoid-like arthritis or acute myocarditis. Clusters of myocarditis cases following Parvovirus B19 infections appeared in a daycare in Thessaloniki in 2024. To molecularly and phylogenetically characterize Parvovirus B19 strains detected during a pediatric outbreak associated with elevated troponin levels and myocarditis in Northern Greece, and to compare these strains with isolates from adult cases with mild symptoms in order to explore potential associations between viral genetic variability and cardiac involvement. MinION sequencing protocol was performed for nine whole blood samples, seven belonging to children with myocarditis, and two to adults presenting mild symptoms. Statistical analysis was performed with QualiMap 2.3 and relevant tools. Phylogenetic analysis identified distinct viral groups originating from the samples investigated. A distinct branch was formed by the reference genome and the ones of the adults’ samples, while samples from children with myocarditis provided discrete branches differing from the reference one. The findings demonstrate a clear association between Parvovirus B19 infection and myocarditis in the pediatric cases analyzed. The detected viral strains, including variants identified in several samples, support the role of Parvovirus B19 as a contributing factor in post-infectious cardiac involvement. Although these results reinforce the clinical relevance of Parvovirus B19 in childhood myocarditis, expanding the sample size would allow for a more robust characterization of circulating strains and confirmation of the observed patterns. Full article

Background/Objectives: It is well documented that people with human immunodeficiency virus (HIV) have nearly twice the risk of incident acute myocardial infarction compared to the general population. The elevated risk stems from a multi-layered interplay of factors such as persistent immune activation inherent to HIV infection and higher prevalence of traditional risk factors associated with nutritional needs. A large proportion of people living with HIV (PWH) reside in Sub-Saharan African countries such as Tanzania; however, there is a dearth of data on nutrition, particularly fruit and vegetable (F&V) intake, a key factor in the prevention of cardiovascular disease (CVD). This study aimed to contribute to the growing literature on CVD prevention for PWH globally. Methods: We conducted secondary analyses of original data collected from a study using the World Health Organization (WHO) STEPS survey among PWH and the general population in Mwanza City between December 2018 and May 2019. Approval for the parent study was obtained from Bugando Medical Center. Multinomial logistic regression analysis examined F&V intake and associated factors between PWH and people living without HIV (PWoH) using sex, employment, and BMI. Results: A total of 537 participants (277 PWoH and 260 PWH) were included in the analysis. PWH were more likely to consume fruits ≥ 4 days per week than PWoH (38% vs. 25%, p = 0.002), whereas vegetable intake did not differ significantly between groups. Fruit intake was higher in males (OR = 5.63; 95% CI: 2.48–12.79) and employed individuals (OR = 3.85; 95% CI: 1.82–8.14). Conclusions: PWH were more likely to consume more fruits than PWoH in this study, a phenomenon that is more novel than previous research. These findings are encouraging to support nutrition-based interventions for PWH who are at a higher risk of CVD. Full article

Transposable elements (TEs) are key regulators of immunity in both health and disease. It has been proven that the activity and transcriptional expression levels of TEs increase during viral infections, correlating with the antiviral response. This study investigates non-LTR TE (LINE, SINE, and SVA) transcriptomic signatures in human PBMCs during infections caused by influenza A virus, HIV, and SARS-CoV-2 (Delta/Omicron variants) using single-cell RNA sequencing (scRNA-seq) data from 98 patients. In the HIV and SARS-CoV-2 patient cohorts, unique cell-specific TE expression patterns were identified that allow for the differentiation of disease severity, prediction of disease progression, and assessment of the therapy’s efficacy. The expression of LINE elements was found to be more dependent on the nature and course of the disease than that of SINE elements. The most variable TE expression profile was observed in precursor cytotoxic T-lymphocytes (T CD8+ Naive cells), which depended on the virus type and the severity of the viral disease. For this cell type, a bioinformatic analysis of the co-expression regulation of TE transcriptional networks and transcription factors during viral infections was performed. This analysis identified key players among those most involved in virus-specific responses, which could serve as diagnostic biomarkers or therapeutic targets for treating diseases caused by influenza A virus, HIV, and SARS-CoV-2. This work confirms the involvement of non-LTR TEs in mediating antiviral responses. Further research into the mechanisms of TE participation in antiviral defense is necessary to recommend them as potential biomarkers for the diagnosis, monitoring, and assessment of antiviral therapy, or as therapeutic targets for viral infections of various origins. Full article

Advances in diagnostic techniques, along with environmental changes driven by human activity, have intensified the surveillance and monitoring of virus and arbovirus circulation on the Amazon. These efforts have increased the detection of insect-specific viruses in field-collected hematophagous arthropods. This study reports the first isolation of the Aguas Brancas virus from mosquitoes collected in the Brazilian Amazon and in a rural area of Brasília, Federal District, Brazil. Arthropods of the family Culicidae, genus Limatus durhamii, were collected at ground level in forest fragments. Sample BEAR812610 originated from Ananindeua, Pará, within the Evandro Chagas Institute’s grounds, and sample BEAR839941 from a forest fragment in Brasília (Ceilândia—Núcleo Rural Boa Esperança, Site B4). Specimens were identified to the species/genus level, macerated, and the supernatant inoculated into C6/36 and Vero cell cultures for viral isolation. The presence of arboviruses was determined by indirect immunofluorescence using antibodies against major arbovirus groups. Positive samples were sequenced for nucleotide and amino acid identification, and phylogenetic analysis confirmed the virus as belonging to the genus Orthoflavivirus. This represents the first report of the isolation and characterization of the insect-specific Aguas Brancas virus. Full article

Potato virus Y (PVY) and potato leafroll virus (PLRV) are the most damaging viruses for potato production worldwide. Mixed infections not only result in additive detrimental effects on plant growth and tuber yield but also complicate the development of durable and broad-spectrum viral resistance. Heterologous protection against PVY can be achieved through the expression of the coat protein (CP) of lettuce mosaic virus (LMV) (CPLMV), conferring resistance via a capsid protein-mediated mechanism. On the other hand, we have previously demonstrated that transgenic lines expressing the PLRV ORF2 (RepPLRV) exhibit resistance to different PLRV isolates. In this study, potato transgenic lines of cv. Kennebec expressing CPLMV and RepPLRV were developed to confer dual virus resistance. Transgenic and non-transgenic control plants were molecularly and phenotypically characterized in greenhouse and field conditions. Across multiple growing seasons, two selected transgenic lines consistently displayed robust resistance to both major viruses, without exhibiting yield penalties or noticeable phenotypic alterations. These results constitute a significant advancement, demonstrating that dual resistance to PVY and PLRV can be achieved while preserving the original agronomic performance of the cultivar. This breakthrough not only contributes to long-term crop productivity but also provides a more sustainable strategy for managing viral diseases in potato production. Full article

The rapid evolution of coronaviruses (CoVs) requires researchers to develop specific yet broad-spectrum detection methods to monitor their constant genomic changes. The goal of the present study was to establish a current pan-coronavirus RT-PCR system capable of detecting a wide variety of CoVs and useful for the investigation of virus diversity and host spectrum. For optimization, one-step and two-step nested RT-PCRs with three RT enzymes were examined, amplifying a ~600 bp long product of the RNA-dependent RNA polymerase. As templates, the in vitro transcribed RNA of ten pathogenic CoVs (SARS-CoV, SARS-CoV-2, NL-63, OC43, feline CoV, porcine epidemic diarrhea virus or PEDV, transmissible gastroenteritis virus or TGEV, canine CoV, bat CoV, and infectious bronchitis virus) were applied instead of the often-used DNA standards. A limit of detection of 5–50 copies/reaction was achieved with a random hexamer-primed two-step RT-PCR and a touchdown cycling profile, representing a lower detection limit and higher specificity compared to previously published primer sets. Swine origin pooled samples (n = 121), collected from apparently healthy herds in Hungary, were tested with the novel RT-PCR system. Sequences of porcine respiratory CoV/TGEV and porcine hemagglutinating encephalomyelitis virus were identified in 24 oral fluid and nasal swab pools, demonstrating the circulation of these viruses in this country, as well as the suitability of the new PCR for their detection. The results highlighted the importance of adequate RT enzyme selection and the use of RNase inhibitors in sample preparation and conservation. Full article

Citrus yellow vein clearing virus (CYVCV) is the causative agent of the yellow vein clearing disease (YVCD), a worldwide and highly destructive disease in lemon (Citrus lemon) and sour orange trees (C. aurantium). The typical symptoms of vein clearing are believed to be associated with CYVCV infection in citrus, so virus-specific diagnostic systems are currently used to confirm infection. In the present study, virome analysis based on high-throughput sequencing (HTS) on a lemon plant showing YVCD revealed mixed infection of CYVCV, iris domestica betaflexyviridae 1 (IDBV), and hop stunt viroid (HSVd). This multiple infection was confirmed in other two lemon plants with similar symptoms using virus/viroid specific primers. This is the first report of IDBV in lemon. Through molecular characterization and the reconstruction of phylogenetic relationships, a possible origin of the viruses/viroid identified in lemon has been hypothesized. Such mixed infections raise new questions about their role in the expression of YVCD symptoms observed on lemon. Full article

Infectious Bronchitis Virus is one of several major viral infections in poultry, affecting the respiratory, reproductive, and renal systems and causing significant economic losses worldwide. Current vaccines, including the H120 strain, provide limited cross-protection against emerging variants, underscoring the need for improved vaccine strategies. In this study, the complete genome of IBV H120 was divided into 12 fragments, synthesized, and assembled using the Golden Gate Assembly (GGA) method. The recombinant virus (rH120) was successfully rescued in chicken fibroblast cells and propagated in embryonated specific-pathogen-free (SPF) chicken eggs. Growth kinetics in embryonated SPF chicken eggs revealed similar replication patterns between rH120 and the original H120 strain. In broiler chickens, rH120 replicated efficiently, as confirmed by viral RNA detection in throat and cloacal swabs, and induced a stronger antibody response by 14 days post-infection. The rH120 virus proved to be genetically stable, infectious, and immunogenic, indicating that GGA-based reverse genetics is an effective system for IBV vaccine development. Full article

Cutaneous viral infections result from the complex interaction between viruses and skin structures, influenced by viral tropism and the host immune response. They can generate lesions ranging from transient rashes to chronic or potentially tumorous formations. Cutaneous manifestations are often the first sign of infection and allow for early recognition. The aim of this review is to analyze the role of viruses in skin pathology, the mechanisms of infection, and the clinical impact. A narrative review of the recent literature was performed, including original articles, systematic reviews, and clinical guidelines on cutaneous viral infections. Data on pathogenic mechanisms, types of lesions, evolution, and therapeutic options were evaluated, covering the main viruses involved in dermatology: herpesviruses, papillomaviruses, poxviruses, and viruses associated with acute rashes. Cutaneous viral infections can be self-limited, recurrent, or chronic, and some can promote malignant transformation of skin cells. The variability of clinical manifestations reflects the virus–host interaction and influences diagnosis and management. Recent advances highlight the development of vaccines and targeted antiviral therapies, which improve prognosis and infection control. Viruses play a major role in the etiology of skin diseases, and their early recognition is essential for preventing complications. Understanding the mechanisms of infection and the cutaneous response contributes to the optimization of therapeutic and preventive strategies, strengthening the modern management of viral cutaneous pathology. Full article

Mammalian placentation represents one of the most striking evolutionary innovations among vertebrates, and accumulating evidence indicates that virus-derived genes—particularly the metavirus-derived PEG10 and PEG11/RTL1—have played indispensable but distinct roles: PEG10 in the emergence of therian viviparity and PEG11/RTL1 in the subsequent differentiation between marsupial and eutherian placental types. Notably, the metavirus-derived SIRH/RTL gene group, which includes PEG10 and PEG11/RTL1, exhibits unique and diverse functions not only in placenta development but also within microglia of the brain. Because microglia originate from yolk sac progenitors, these findings suggest that extraembryonic tissues such as the placenta and yolk sac provided permissive environments that enabled the retention, expression and functional domestication of virus-derived sequences. Once the placenta itself was established through viral gene integration, it may in turn have acted as a powerful driver of eutherian evolution through recurrent acquisition and co-option of additional virus-derived genes—a process we refer to as “placenta-driven evolution.” This perspective offers a unified framework in which viral gene acquisition is viewed as a key driver of genomic innovation, tightly intertwined with the emergence of viviparity, subsequent divergence at the marsupial–eutherian split, and continued diversification of placental structure and function across eutherian lineages. Full article

Influenza A viruses exhibit broad host tropism, infecting multiple species including humans, avian species, and swine. Swine influenza virus (SIV), while primarily circulating in porcine populations, demonstrates zoonotic potential with sporadic human infections. In this investigation, we identified two H1N1 subtype swine influenza A virus strains designated A/swine/China/SD6591/2019(H1N1) (abbreviated SD6591) and A/swine/China/SD6592/2019(H1N1) (abbreviated SD6592) in Shandong Province, China. The GenBank accession numbers of the SD6591 viral gene segments are PV464931-PV464938, and the GenBank accession numbers corresponding to each of the eight SD6592 viral gene segments are PV464939-PV464946. Phylogenetic and recombination analyses suggest potential evolutionary differences between the isolates. SD6591 displayed a unique triple-reassortant genotype: comparative nucleotide homology assessments demonstrated that the PB2, PB1, NP, NA, HA, and NEP genes shared the highest similarity with classical swine-origin H1N1 viruses. In contrast, SD6592 maintained genomic conservation with previously characterized H1N1 swine strains, although neither of these two isolates exhibited significant intrasegmental recombination events. Through comprehensive sequence analysis of these H1N1 SIVs, this study provides preliminary insights into their evolutionary history and underscores the persistent risk of cross-species transmission at the human–swine interface. These findings establish an essential foundation for enhancing national SIV surveillance programs and informing evidence-based prevention strategies against emerging influenza threats. Full article

The historic Rockborn strain of the canine distemper virus was widely used as a vaccine, but its use was discontinued due to safety concerns. Yet, Rockborn-like canine distemper virus strains are still used in some vaccine formulations. Genetic analysis of this strain was previously limited to the H gene, leaving its full evolutionary and pathogenic potential unclear. This study aimed to determine the complete genome sequence of the Rockborn strain to reconstruct its origin, understand its evolution, and provide a reference for improving diagnostics and future research on virulence markers. An amplicon-based sequencing protocol using MinION nanopore technology was employed to determine the complete genome of the Rockborn-46th laboratory strain. The genome was assembled, annotated, and analyzed in comparison with 223 genomes. The complete genome of the Rockborn strain was 15,690 nucleotides in length. Phylogenetic analysis revealed that Rockborn forms a unique lineage with field isolates from a masked civet in China and a dog in the United States. Crucially, a significant recombination event was identified, showing that the Rockborn strain acted as a parental strain, contributing its F and H genes to create mosaic viruses. The full-genome characterization of the Rockborn strain confirms that Rockborn-like viruses persist and actively contribute to the evolution of canine distemper virus through recombination. This finding highlights the inadequacy of single-gene analysis for diagnostics and surveillance, and underscores the necessity of whole-genome sequencing to accurately track the virus epidemiology and evolution. Full article

Circulating recombinant forms (CRFs) are important components of the HIV-1 pandemic. Previous studies have reported the propagation of diverse HIV-1 CRFs of South American origin in Europe. Here, through protease-reverse transcriptase (Pr-RT) and integrase sequence analyses, we identify a Spanish cluster (BC3) branching with a Brazilian virus (10BR_RJ009) previously classified as CRF146_BC. In Pr-RT, BC3 comprised 14 viruses and was nested within a larger cluster, comprising 22 Brazilian viruses and 1 Spanish virus branching outside of BC3. Near full-length genome analyses of five BC3 viruses revealed mosaic structures identical to 10BR_RJ009, with two breakpoints delimiting a ~0.3 kb subtype B fragment within an otherwise subtype C genome. Two other Brazilian viruses previously classified as CRF146_BC (10BR_RJ039 and 01_BR_RGS69) had one and two additional short subtype B fragments, respectively, and failed to group with the 10BR_RJ009/BC3 cluster in subtype C fragments. Based on these results, we contend that 10BR_RJ009 and BC3 viruses, but not 10BR_RJ039 and 01_BR_RGS69, should be classified as CRF146_BC. Bayesian analyses estimated the CRF146_BC emergence in Brazil to be around 1999 and its introduction in Europe around 2011. CRF146_BC is the 10th CRF of South American origin reported to circulate in Europe, reflecting the relationship between South American and European HIV-1 epidemics. Full article