Chronic Hepatitis B Genotype C Mouse Model with Persistent Covalently Closed Circular DNA.

Hepatitis B virus (HBV) can cause chronic infections, significantly increasing the risk of death from cirrhosis and hepatocellular carcinoma (HCC). A key player in chronic HBV infection is covalently closed circular DNA (cccDNA), a stable episomal form of viral DNA that acts as a persistent reservoir in infected hepatocytes and drives continuous viral replication. Despite the development of several animal models, few adequately replicate cccDNA formation and maintenance, limiting our understanding of its dynamics and the evaluation of potential therapeutic interventions targeting cccDNA.

Comparative Evolutionary Epidemiology of SARS-CoV-2 Delta and Omicron Variants in Kuwait.

Continuous surveillance is critical for early intervention against emerging novel SARS-CoV-2 variants. Therefore, we investigated and compared the variant-specific evolutionary epidemiology of all the Delta and Omicron sequences collected between 2021 and 2023 in Kuwait. We used Bayesian phylodynamic models to reconstruct, trace, and compare the two variants' demographics, phylogeographic, and host characteristics in shaping their evolutionary epidemiology.

Rewriting Viral Fate: Epigenetic and Transcriptional Dynamics in KSHV Infection.

Kaposi's sarcoma-associated herpesvirus (KSHV), a γ-herpesvirus, is predominantly associated with Kaposi's sarcoma (KS) as well as two lymphoproliferative disorders: primary effusion lymphoma (PEL) and multicentric Castleman disease (MCD). Like other herpesviruses, KSHV employs two distinct life cycles: latency and lytic replication. To establish a lifelong persistent infection, KSHV has evolved various strategies to manipulate the epigenetic machinery of the host.

Detection of Hepatitis C Virus Infection from Patient Sera in Cell Culture Using Semi-Automated Image Analysis.

The study of hepatitis C virus (HCV) replication in cell culture is mainly based on cloned viral isolates requiring adaptation for efficient replication in Huh7 hepatoma cells. The analysis of wild-type (WT) isolates was enabled by the expression of SEC14L2 and by inhibitors targeting deleterious host factors. Here, we aimed to optimize cell culture models to allow infection with HCV from patient sera.

The Epidemiology, Clinical, and Economic Burdens of Respiratory Syncytial Virus Infections Amongst Hospitalized Children Under 5 Years of Age in Jordan: A National Multi-Center Cross-Sectional Study.

Respiratory syncytial virus (RSV) has been recognized as a highly important cause of morbidity and mortality among children and adults. A cross-sectional study at representative sites in Jordan was undertaken to provide an assessment of the epidemiology and health and economic burdens of RSV and influenza infections in Jordan amongst hospitalized children under 5 years old for the period between 15 November 2022 and 14 April 2023. This study involved 1000 patients with a mean age of 17.

First Report of Influenza D Virus in Dairy Cattle in Pakistan.

Influenza D virus (IDV) is a newly emerged zoonotic virus increasingly reported worldwide. Cattle are considered the main reservoir of IDV, although it was first isolated from pigs. IDV infects multiple animal species and contributes to the bovine respiratory disease complex (BRDC).

Integrating Interpretability in Machine Learning and Deep Neural Networks: A Novel Approach to Feature Importance and Outlier Detection in COVID-19 Symptomatology and Vaccine Efficacy.

In this study, we introduce a novel approach that integrates interpretability techniques from both traditional machine learning (ML) and deep neural networks (DNN) to quantify feature importance using global and local interpretation methods. Our method bridges the gap between interpretable ML models and powerful deep learning (DL) architectures, providing comprehensive insights into the key drivers behind model predictions, especially in detecting outliers within medical data. We applied this method to analyze COVID-19 pandemic data from 2020, yielding intriguing insights.

Development of a Multiplex RT-PCR Detection for Six Viruses Infecting Strawberry.

Strawberry viruses are significant pathogenic agents in strawberry. The development and application of efficient virus detection technology can effectively reduce the economic losses incurred by virus diseases for strawberry cultivators. In order to rapidly identify strawberry virus species and prevent the spread of virus disease, a multiplex reverse transcription polymerase chain reaction system was established for the simultaneous detection and identification of strawberry mild yellow edge virus (SMYEV), strawberry vein banding virus (SVBV), strawberry mottle virus (SMoV), strawberry polerovirus 1 (SPV-1), strawberry pallidosis-associated virus (SPaV), and strawberry crinivirus 4 (SCrV-4).

Virulence and Replicative Fitness of HIV-1 Transmitted/Founder (T/F) Viruses Harbouring Drug Resistance-Associated Mutation.

The biological characteristics of early transmitted/founder (T/F) variants are crucial factors for viral transmission and constitute key determinants for the development of better therapeutics and vaccine strategies. The present study aimed to generate T/F viruses and to characterize their biological properties. For this purpose, we constructed 18 full-length infectious molecular clones (IMCs) of HIV from recently infected infants.

Predictive Efficacy of Dual Therapies Combining Integrase Strand Transfer Inhibitors with Second-Generation Non-Nucleoside Reverse Transcriptase Inhibitors Following HIV-1 Treatment Failure in Cameroon: Implications for the Use of a Long-Acting Therapeutic Strategy in Low- and Middle-Income Countries.

Dual therapies (DT) combining integrase strand transfer inhibitors (INSTIs) with second-generation non-nucleoside reverse transcriptase inhibitors (2nd-Gen-NNRTIs) offer new possibilities for HIV treatment to improve adherence. However, drug resistance associated mutations (RAMs) to prior antiretrovirals may jeopardize the efficacy of DT. We herein describe the predicted efficacy of DT combining INSTIs + 2nd-Gen-NNRTI following treatment failure among Cameroonian patients.

Isothermal Nucleic Acid Amplification for Point-of-Care Primary Cervical Cancer Screening.

Human Papillomavirus (HPV) infection is a significant global health concern linked to various cancers, particularly cervical cancer. Timely and accurate detection of HPV is crucial for effective management and prevention strategies. Traditional laboratory-based HPV testing methods often suffer from limitations such as long turnaround times, restricted accessibility, and the need for trained personnel, especially in resource-limited settings.

A Possible Protective Effect of IgA Against Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) in Bronchoalveolar Lavage in COVID-19 Patients Admitted to Intensive Care Unit.

SARS-CoV-2 infection induces a humoral immune response, producing virus-specific antibodies such as IgM, IgG, and IgA. IgA antibodies are present at mucosal sites, protecting against respiratory and other mucosal infections, including SARS-CoV-2, by neutralizing viruses or impeding attachment to epithelial cells. Since SARS-CoV-2 spreads through the nasopharynx, the specific IgAs of SARS-CoV-2 are produced quickly after infection, effectively contributing to virus neutralization.

Phylogeography and Evolutionary Dynamics of Tobacco Curly Shoot Virus.

Tobacco curly shoot virus (TbCSV), a begomovirus, causes significant economic losses in tobacco and tomato crops across East, Southeast, and South Asia. Despite its agricultural importance, the evolutionary dynamics and emergence process of TbCSV remain poorly understood. This study analyzed the phylodynamics of TbCSV by examining its nucleotide sequences of the coat protein (CP) gene collected between 2000 and 2022.

Evaluating the Impact of N-Glycan Sequon Removal in the p27 Peptide on RSV F Protein Immunogenicity and Functionality.

Respiratory syncytial virus (RSV) is the leading cause of acute lower respiratory tract infections in young children, elderly and immunocompromised patients worldwide. The RSV fusion (F) protein, which has 5-6 N-glycosylation sites depending on the strain, is a major target for vaccine development. Two to three of these sites are located in the p27 peptide, which is considered absent in virions.

The Laboratory Opossum () Is a Unique Model for Research on Zika Virus: Robust Immune Response, Widespread Dissemination, and Long-Term Persistence.

The Zika virus (ZIKV) epidemic elicited a rapid commitment to the development of animal models for ZIKV research. Non-human primates (NHPs) and mice have made significant contributions to this research, but NHPs are expensive, have a long gestation period, and are available only in small numbers; non-genetically modified mice are resistant to infection. To address these deficiencies, we have established the laboratory opossum, , as a small animal model that complements the mouse and monkey models.

Emergence of Bluetongue Virus Serotype 3 in Portugal (2024).

In September 2024, bluetongue virus serotype 3 (BTV-3) was first identified in Portugal, specifically in the Alentejo region (Évora District), using molecular diagnostic methods. The initial case involved a sheep exhibiting severe clinical symptoms, including head oedema, prostration, nasal discharge, and significant respiratory distress. A subsequent case was documented in another sheep from a different farm within the same district, which presented with high fever (41.

Efficiency of Bacteriophage-Based Detection Methods for Non-Typhoidal in Foods: A Systematic Review.

Food contamination with non-typhoidal (NTS) presents a significant public health risk, underscoring the critical need for rigorous food safety measures throughout the production, distribution, preparation, and consumption stages. Conventional diagnostic strategies are time-consuming and labor-intensive and are thus sub-optimal for throughput NTS detection. Bacteriophages (phages) are highly specialized bacterial viruses and exhibit extreme specificity for their hosts.

Assessment of Favipiravir and Remdesivir in Combination for SARS-CoV-2 Infection in Syrian Golden Hamsters.

Favipiravir (FVP) and remdesivir (RDV) have demonstrable antiviral activity against SARS-CoV-2. Here, the efficacy of FVP, RDV, and FVP with RDV (FVP + RDV) in combination was assessed in Syrian golden hamsters challenged with SARS-CoV- 2 (B.1.

Conformational Flexibility in Capsids Encoded by the .

Caliciviruses are a diverse group of non-enveloped, positive-sense RNA viruses with a wide range of hosts and transmission routes. Norovirus is the most well-known member of the ; the acute gastroenteritis caused by human norovirus (HuNoV), for example, frequently results in closures of hospital wards and schools during the winter months. One area of calicivirus biology that has gained increasing attention over the past decade is the conformational flexibility exhibited by the protruding (P) domains of the major capsid protein VP1.

Exclusion of Superinfection or Enhancement of Superinfection in Pestiviruses-APPV Infection Is Not Dependent on ADAM17.

Some viruses can suppress superinfections of their host cells by related or different virus species. The phenomenon of superinfection exclusion can be caused by inhibiting virus attachment, receptor binding and entry, by replication interference, or competition for host cell resources. Blocking attachment and entry not only prevents unproductive double infections but also stops newly produced virions from re-entering the cell post-exocytosis.

Innate Immune Response Against Batai Virus, Bunyamwera Virus, and Their Reassortants.

(OBVs) represent a diverse group of RNA viruses, encompassing a progressively increasing number of arboviruses that cause disease in both humans and livestock. Yet, studies investigating these viruses remain scarce despite the critical importance of such knowledge for assessing their zoonotic potential. In this study, we conducted an evaluation of the early immune response against the understudied Batai virus (BATV), as well as the influence of reassortment with the Bunyamwera virus (BUNV) on this response.

Special Issue "Host Targeted Therapeutics Against Virus Infections".

The COVID-19 pandemic, along with the emergence and sustained transmission of highly pathogenic avian influenza viruses (H5N1) in U [...

Comparative Evaluation of Open-Source Bioinformatics Pipelines for Full-Length Viral Genome Assembly.

The increasingly widespread application of next-generation sequencing (NGS) in clinical diagnostics and epidemiological research has generated a demand for robust, fast, automated, and user-friendly bioinformatics workflows. To guide the choice of tools for the assembly of full-length viral genomes from NGS datasets, we assessed the performance and applicability of four open-source bioinformatics pipelines (shiver-for which we created a user-friendly Dockerized version, referred to as dshiver; SmaltAlign; viral-ngs; and V-pipe) using both simulated and real-world HIV-1 paired-end short-read datasets and default settings. All four pipelines produced consensus genome assemblies with high quality metrics (genome fraction recovery, mismatch and indel rates, variant calling F1 scores) when the reference sequence used for assembly had high similarity to the analyzed sample.

Probability of Starting Two-Drug Regimen (2DR) vs. Three-Drug Regimen (3DR) in ART-Naïve and ART-Experienced Person with HIV (PWH) Across the First Wave of COVID-19 Pandemic.

: This study examined the impact of the COVID-19 lockdown on antiretroviral therapy (ART) prescriptions among persons living with HIV (PWH) in Italy. : Data from the ICONA cohort included ART-naïve individuals who started ART between January 2019 and December 2022, and ART-experienced individuals who started new ART with HIV RNA ≤50 cps/mL from January 2016 to December 2022. The analysis focused on the proportion of PWH starting or switching to dual (2DR) versus triple (3DR) ART regimens.

A Mutation in the Herpes Simplex Virus Type 1 (HSV-1) UL29 Gene is Associated with Anti-Herpesvirus Drugs' Susceptibility.

Herpes simplex virus type 1 (HSV-1) acyclovir (ACV) resistance is acquired by mutations in the viral thymidine kinase (TK) or DNA polymerase (DNApol) genes. We previously obtained an ACV-resistant clone (HSV-1_VZV_TK_clone α) by sequential passages of HSV-1_VZV-TK, a recombinant virus which lacked its endogenous TK activity and instead expressed the varicella-zoster virus (VZV) TK ectopically. HSV-1_VZV_TK_clone α had been generated using an HSV-1_BAC in the presence of increasing concentrations of ACV.