Viruses-Basel最新文献

The concentration of extracellular vesicles (EVs) in the peripheral blood of COVID-19 patients is increased. Nevertheless, their potential role in the transmission of infection remains unclear. This study was performed to determine whether EVs produced by the sub-genomic replicon system developed in Baby Hamster Kidney (BHK-21) cells could transfer SARS-CoV-2 replicon RNA, leading to the establishment of a viral replication system in human cells. Purified EVs from the SARS-CoV-2 sub-genomic replicon cell line BHK-21 were cultured with a naive human cell line. The success of EV-mediated transfer of SARS-CoV-2 replicon RNA and its productive replication was assessed using G-418 selection, a luciferase assay, immunostaining, and Western blot. We found that the A549 cell line cultured with EVs isolated from SARS-CoV-2 BHK-21 replicon cells developed G-418-resistant cell colonies. SARS-COV-2 RNA replication in A549 cells was confirmed by nano luciferase, Nsp1 protein. SARS-CoV-2 RNA replication causes massive morphological changes. Treatment of cells with the FDA-approved Paxlovid demonstrated a dose-dependent inhibition of viral replication. We isolated two human epithelial cell lines (gastrointestinal and neuroblastoma) and one vascular endothelial cell line that stably support high-level replication of SARS-CoV-2 sub-genomic RNA. Viral elimination did not revert the abnormal cellular shape, vesicle accumulation, syncytia formation, or EV release. Our study's findings highlight the potential implications of EV-mediated transfer of replicon RNA to permissive cells. The replicon model is a valuable tool for studying virus-induced reversible and irreversible cellular reprogramming, as well as for testing novel therapeutic strategies for SARS-CoV-2.

Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, has had major social and economic consequences worldwide. Whole genome sequencing (WGS) is essential for genomic monitoring, enabling tracking of viral evolution, detection of emerging variants, and identification of introductions and transmission chains to inform timely public health responses. Here, we compile and harmonize SARS-CoV-2 genomic data generated by multiple laboratories across Kazakhstan together with publicly available sequences to provide a national overview of genomic dynamics across successive epidemic waves from 2020 to 2022. We analyzed 4462 genomes deposited in GISAID (including 340 generated in this study), of which 3299 passed Nextclade quality filters, and summarized lineage turnover across major phases (pre-VOC, Alpha, Delta, Omicron BA.1/BA.2, Omicron BA.4/BA.5, and a later recombinant-dominant period). Sequencing intensity varied markedly over time (0.60‱ of confirmed cases during Delta vs. 11.57‱ during the Omicron BA.5 wave), suggesting that lineage diversity and persistence may be underestimated. Pre-VOC circulation included ≥12 Pango lineages with evidence of multiple introductions and sustained local transmission, including a Kazakhstan-restricted B.4.1 lineage that emerged in Nur-Sultan/Astana and disappeared after April 2020. The Tengizchevroil oilfield outbreak comprised B.1.1 viruses with phylogenetic support for ≥three independent introductions. Alpha and Omicron waves were characterized by repeated introductions and heterogeneous origins, whereas Delta was dominated by AY.122 with an additional distinct AY.122 cluster; a notable BF.7 local transmission event was observed during BA.5. We also highlight locally enriched non-lineage-defining mutations. Overall, recurrent importations and variable local amplification shaped SARS-CoV-2 dynamics in Kazakhstan, while interpretation is constrained by strongly time-skewed sequencing.

Influenza A virus expresses three envelope proteins, hemagglutinin (HA), neuraminidase (NA), and matrix protein 2 (M2). Of these, HA and NA associate with lipid rafts, whereas M2 remains in the peri-raft region. One reason for the lipid raft association of HA and NA is that they possess longer transmembrane domains (TMDs) (27 and 29 amino acids, respectively) than that of M2 (19 amino acids). Moreover, M2 localizes in the peri-raft region, despite the presence of some lipid raft-targeting features. Therefore, we introduced amino acid insertions into the N-terminal region of M2 to increase the TMD length to 22, 25, and 27 residues, and evaluated these M2-TMD mutants for their association with lipid rafts and impact on virus replication. Confocal microscopy, immunoprecipitation, and cell cytotoxicity assays showed that the cell surface expression and cytotoxic potential of M2-TMD mutants were comparable to those of wildtype M2. Based on the Triton X-100 solubility assay and colocalization analysis between lipid rafts and M2-TMD mutants, we found that the mutant proteins largely remained localized in non-raft domains. Importantly, an increase in M2-TMD length negatively influenced viral replication. These findings suggest that M2-TMD length is optimized for its proper function and does not determine its association with lipid raft domains.

Background: Viral respiratory tract infections (RTIs) frequently lead to emergency department (ED) presentations and hospital admissions, particularly among older adults and individuals with underlying health conditions. Identifying patients at increased risk for hospitalization is essential for optimizing triage and resource allocation. This study aimed to determine independent demographic, clinical, and virological predictors of hospital admission among adults presenting with confirmed viral RTIs.

Methods: A retrospective cohort study was conducted at a tertiary hospital between September 2022 and May 2024. Adult patients with molecularly confirmed viral RTIs were included. Demographic, clinical, and microbiological data were extracted from electronic medical records. Predictors of admission were assessed using univariate and multivariate logistic regression.

Results: Among 311 patients, 147 (47.3%) required hospitalization. Hospitalized patients were significantly older and more likely to present with fever, cough, tachypnea, dyspnea, chest pain, comorbidities, and lower or mixed respiratory tract infections (all p < 0.001). In multivariate analysis, older age, fever, cough, and lower or mixed RTIs were strong independent predictors of admission. Several viral pathogens, including human rhinovirus, non-SARS-CoV-2 coronaviruses, influenza A, and parainfluenza virus, were associated with reduced odds of hospitalization.

Conclusions: Age, comorbidity burden, and lower respiratory tract involvement are key determinants of hospitalization in viral RTIs. Integrating clinical and virological data may improve risk stratification and guide ED triage during seasonal and emerging respiratory virus activity.

In this study, we constructed plasmids to increase the overall expression level of the SARS-CoV-2 S-protein and its presentation on the cell surface. To this end, we designed a series of plasmid constructs encoding the SARS-CoV-2 S-protein with modifications to its cytoplasmic domain and containing various 5' and 3' untranslated regions. Our results confirmed the critical role of the S-protein cytoplasmic domain in limiting its localization to the cell surface. We confirmed that deletion of the 19 C-terminal amino acids, which contain an endoplasmic reticulum retrieval signal, significantly increased S-protein presentation on the cell surface. Furthermore, introducing the HuR-binding site from the CD47 3' untranslated region and replacing the 19 C-terminal amino acids of the S-protein with the CD47 cytoplasmic tail significantly enhanced total S-protein expression compared to the wild-type S-protein and constructs with the 19-amino-acid deletion. Unfortunately, for the plasmid constructs bearing CD47 elements, their higher surface expression compared to the wild-type S-protein correlated with a high total protein expression level.

Human adenoviruses (HAdVs) are globally distributed pathogens capable of causing a wide range of clinical manifestations, particularly acute respiratory infections. However, their genomic diversity remains insufficiently characterized, with substantial geographic gaps in available sequence data, including for Russia, where only a few complete genomes have been deposited prior to this work. In this study, we analyzed more than 1200 PCR-positive respiratory specimens collected from hospitalized patients within routine surveillance projects and the Global Influenza Hospital Surveillance Network (GIHSN) across plenty of Russian regions during 2023-2024. Virus isolation followed by next-generation sequencing yielded 128 complete HAdV genomes representing species B, C, and D. The dataset included 27 B3, 9 B7, 44 B55, 12 C1, 16 C2, 4 C5, 7 C89, 5 C108, and one D109 genome, as well as three unassigned recombinant viruses with p89h5f5, p5h6f6 and p5h57f6 genomic structures (p, penton base; h, hexon; f, fiber). Phylogenetic analyses of whole genomes and capsid genes revealed extensive variability in immunogenic regions, particularly in species C, and identified clusters within B3 viruses. Notably, HAdV-D109 was identified in Russia, marking only the second reported detection of this genotype worldwide. Together, these findings substantially expand the currently available genomic landscape of HAdVs, highlighting the circulation of diverse and recombinant strains in Russia.

Rotavirus (RV) is the primary cause of severe gastroenteritis in young children, yet the long noncoding RNA (lncRNA) regulatory landscape governing the host response remains largely unmapped. To address this gap, the present study performed an integrated transcriptomic analysis of mRNA and lncRNA expression profiles in RV-infected MA104 cells at 24 h post-infection. Deep sequencing identified 11,919 high-confidence lncRNAs, revealing a massive transcriptional shift: 3651 mRNAs and 4655 lncRNAs were differentially expressed, with both populations predominantly upregulated. Functional enrichment analysis confirmed the strong activation of key innate immunity pathways, including the RIG-I-like receptor, Toll-like receptor, and TNF signaling pathways. Conversely, fundamental metabolic pathways were found to be suppressed. Crucially, the analysis of lncRNA targets highlighted their involvement in coordinating the host antiviral defense, particularly through transregulation. Experimental validation confirmed the significant upregulation of key immune-related mRNAs (OASL and C3) as well as two novel lncRNAs (lncRNA-6479 and lncRNA-4290) by qRT-PCR. The significant upregulation of OASL and C3 was validated at the protein level, confirming the biological relevance of the transcriptomic data. This study provides a foundational, genome-wide resource, identifying novel lncRNA targets for future mechanistic investigation into host-RV interactions.

Background: Acute viral respiratory infections are a major cause of morbidity among young children, with respiratory syncytial virus (RSV) being the leading pathogen. In Jordan and globally, most RSV research has focused on hospitalized patients, while data from emergency departments (EDs) and outpatient settings remain limited.

Methods: This cross-sectional study was conducted at two major Jordanian hospitals between November 2022 and March 2023. Children under five years of age presenting to EDs or outpatient clinics with symptoms of acute respiratory infection were enrolled. Nasopharyngeal specimens were tested for RSV, and subtypes (RSV-A and RSV-B) were identified using multiplex RT-PCR.

Results: Of 229 enrolled children, 92 (40.2%) tested positive for RSV, with RSV-B accounting for 81.5% of positive cases. RSV positivity was higher in ED presentations than in outpatient clinics (46% vs. 35%). Wheezing (72.8% vs. 39.4%, p < 0.001) and dyspnea (33.7% vs. 14.6%, p = 0.001) were significantly more frequent among RSV-positive patients. Independent predictors of RSV positivity included non-referred outpatient visits (OR = 15.26), non-referred ED visits (OR = 42.93), younger age, and prior systemic steroid use.

Conclusions: RSV poses a substantial burden in outpatient and ED settings. Identified demographic and clinical predictors may help target high-risk groups for future preventive interventions.

Aquatic ecosystems host the planet's greatest animal diversity, and with it, a remarkably varied virosphere [...].

The COVID-19 pandemic and subsequent non-pharmaceutical interventions (NPIs) significantly disrupted the epidemiology of pediatric respiratory viruses. This study compared infection patterns among 3658 hospitalized children in South Korea during the pandemic (2020-2022) and the post-emergency phase (2023-2024), following the relaxation of mandatory NPIs. Of 4419 eligible tests, the most frequently detected viruses overall were rhinovirus/enterovirus (HRV/HEV) (27.9%), influenza (14.5%), and respiratory syncytial virus (RSV, 11.9%). The post-emergency phase was marked by a dramatic surge in influenza virus (IFV), which surged dramatically (5.5% → 28.2%), and a more than two-fold increase in adenovirus (ADV) (5.7% → 12.5%) (p < 0.001). (p < 0.001). Conversely, parainfluenza virus (PIV) detection rates declined significantly (15.4% → 11.3%, p < 0.001). Demographically, post-emergency phase patients were significantly older (mean 4.9 vs. 3.5 years) and experienced a shorter hospital stays (3.2 vs. 4.3 days) (p < 0.001). Crucially, age-specific susceptibility shifts were evident. IFV rebounded across all pediatric ages but spiked severely in school-aged children and adolescents, while HRV/HEV demonstrated a clear proportional shift towards older age groups. These results demonstrate a substantial reconfiguration of the pediatric respiratory landscape, necessitating age-stratified surveillance and flexible public health strategies to mitigate the future infectious disease burden.