Search Results (1,952)

Objective: The classification of hereditary spastic paraplegia (HSP) is based on genetics, and the number of genetic loci continues to increase with new genetic descriptions. Additionally, the number of new variants in known mutations continues to increase. In this paper, we aim to report our experience with genetically confirmed HSPs. Methods: We retrospectively evaluated 10 consecutive children with genetically confirmed HSPs. Results: In this study, we identified six novel mutations, including spastic paraplegia 11 (SPG11), glucosylceramidase beta 2 (GBA2), chromosome 19 open reading frame 12 (C19orf12), 1 in each of the Cytochrome P450 family 7 subfamily B member 1 (CYP7B1) genes, and two different mutations in the intropomyosin-receptor kinase fused gene (TFG) gene. We also identified different clinical phenotypes associated with known mutations. Conclusions: Heterozygous mutations with GBA2 and SPG11 mutation-related HSP are reported for the first time, expanding the known inheritance patterns. We report a novel homozygous chromosome 19 open reading frame 12 (C19orf12) mutation resulting in iron accumulation in the brain, broadening the genetic variants and clinical findings. We determine the first Turkish patients with carnitine palmitoyltransferase IC (CPT1C) and TFG gene mutation-related pure HSP. A pure form of HSP with two novel TFG gene mutations is also identified for the first time. We report the first Turkish patient with kinase D-interacting substrate of 220 kDa (KIDINS220) gene, broadening the clinical spectrum of KIDINS220 variant-related disorders to encompass certain HSPs. Moreover, a novel variant in the oxysterol7-hydroxylase (CYP7B1) gene is reported, expanding the genetic variants and clinical findings relating to SPG5. Full article

Background/Objectives: Prenatal exposure to famine can lead to lasting health effects through changes in DNA methylation. This study aims to evaluate the impact of prenatal exposure to the Chinses Great Famine (1959–1961) on human epigenome and the subsequent influence on blood lipids. Methods: We conducted an epigenome-wide association study (EWAS) of peripheral blood-based DNA methylation and prenatal exposure to the Chinese Great Famine as well as blood lipids among eight participants exposed to famine and eight sex-matched participants (born ≤ 3 years after the famine). Genome-wide DNA methylation sites were profiled using the Illumina EPIC BeadChip, which covers 850K methylation positions. Results: After EWAS analyses, seven probes in genes C8orf31, ELAVL1, U6, GBA2, SHOX2, SLC1A4, and NPHP4 reached p < 1 × 10⁻⁵. Of these, famine exposure was associated with decreased methylation levels of a GBA2 exonic probe cg08258661 (p = 4.9 × 10⁻⁶). After false discovery rate (FDR) correction, pathway enrichment analyses for genes harboring nominally significant (p < 0.05) probes identified 44 significant pathways (q < 0.05), and 5 pathways were related to lipid metabolism. After FDR correction in each pathway, probes cg02622866 (5’UTR of ATF2, p = 1.09 × 10⁻³), cg07316730 (body of GRB2, p = 1.32 × 10⁻³), and cg01105385 (body of PIK3R1, p = 1.94 × 10⁻³) in the PI2K-Akt signaling pathway were associated with blood LDL-C (q ≤ 0.04); probes cg09180702 (3’UTR of PIGQ, p = 9.21 × 10⁻⁵, and q = 0.04) and cg01421548 (body of HS3ST4, p = 5.23 × 10⁻⁵, and q = 0.01) in the metabolism pathway were associated with blood LDL-C and HDL-C, respectively; In addition, probe cg08460387 (5’UTR of MAN1C1, p = 1.09 × 10⁻⁴, and q = 0.02) in the vesicle-mediated transport pathway was associated with log-transformed blood triglycerides. Conclusions: Through an epigenetic study of the Chinese Great Famine, we identified six novel genes involved in lipid metabolism. Full article

Since the appearance of the Severe Acute Respiratory Syndrome (SARS) virus, there has been increased interest in understanding the role of bats in the maintenance and circulation of coronaviruses. This study aimed to describe the phylogenetic and evolutionary relationships and antigenic architecture of a new coronavirus detected in bats in the Department of Córdoba. In a surveillance study of pathogens of interest to public health, a bat Phyllostomus hastatus was captured. Rectal swabs samples were collected from the bats, and RNA was extracted and sequenced using NGS with MGI-G50 equipment. The results were analyzed using bioinformatics software. A contig of 28,619 nucleotides associated with the Coronaviridae family was obtained. Phylogenetic and molecular clock analyses of the ORF1ab gene revealed a novel divergent Alphacoronavirus that originated directly from an ancestral node. The analysis of the spike (S) protein and receptor-binding domain (RBD) is similar to that of humans (HCoV-229E) and porcine coronaviruses. In silico analysis suggests potential RBD interaction sites with human and pig cellular receptor aminopeptidase N. There is a possible risk of interspecies jumping of the new AlphaCoV/P. hastatus in humans and pigs. This is the first study to perform phylogenetic, evolutionary, and antigenic characterization of bat coronaviruses in Colombia. Full article

Background: Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are recognized as a spectrum of neurodegenerative disorders with overlapping clinical, pathological, and genetic features. The identification of C9orf72 hexanucleotide repeat expansion as the most common genetic cause of both conditions has prompted further investigation of genetic modifiers that may contribute to disease heterogeneity. We aimed to analyze the frequency of C9orf72 repeat expansions and potential modifying roles of APOE, ATXN1, and ATXN2 in Serbian ALS/FTD patients. Methods: Our study included an ALS/FTD cohort (n = 22) and healthy controls (n = 94). Repeat sizing in C9orf72, ATXN1 and ATXN2 was performed by fluorescent polymerase chain reaction (PCR) and capillary electrophoresis, while repeat-primed PCR was used to confirm C9orf72 expansions. APOE genotyping was conducted using real-time PCR assays targeting SNPs rs429358 and rs7412. Results: In the ALS/FTD cohort, 31.82% of the patients had heterozygous C9orf72 repeat expansion. The most common APOE genotype among patients was ε3/ε3 (72.73%). Intermediate-length ATXN1 alleles (32–44 repeats) were detected in 13.64% of patients and ATXN2 intermediate-length alleles (27–33 repeats) were found in 9% of patients. No significant differences were observed between ALS/FTD patients and controls in APOE ε4 frequency or intermediate ATXN1/ATXN2 repeats. Conclusions: Larger, population-specific studies and meta-analyses are needed to better understand the role of genetic modifiers in ALS/FTD pathogenesis and their influence on clinical heterogeneity. By integrating genetic and clinical data, this study represents a step toward the development of precision medicine strategies for ALS/FTD. Full article

Porcine Reproductive and Respiratory Syndrome (PRRS) causes significant economic losses in the swine industry. Circular RNAs (circRNAs), a class of stable non-coding RNAs, are increasingly recognized as regulators in immune responses and host–virus interactions. This study investigated the genome-wide circRNA responses in porcine alveolar macrophages (PAMs), key cell targets of PRRSV, following treatment with a modified live virus (MLV) vaccine or two interferon (IFN) subtypes (IFN-α1, IFN-ω5). Using RNA sequencing, we identified over 1000 differentially expressed circRNAs across treatment groups, revealing both conserved and distinct expression profiles. Gene Ontology and KEGG pathway analyses indicated that circRNA-associated genes are significantly enriched in immune-related processes and pathways, including cytokine signaling and antiviral defense. Notably, IFN-ω5 treatment induced a pronounced circRNA response, aligning with its potent antiviral activity. We further explored the regulatory potential of these circRNAs by predicting miRNA binding sites, revealing complex circRNA-miRNA interaction networks. Additionally, we assessed the coding potential of differentially expressed circRNAs by identifying open reading frames (ORFs), internal ribosome entry sites (IRESs), and N6-methyladenosine (m⁶A) modification sites, suggesting a subset may undergo non-canonical translation. These findings provide a comprehensive landscape of circRNA expression in PAMs under different antiviral conditions, highlighting their potential roles as immune regulators and novel players in interferon-mediated antiviral responses, particularly downstream of IFN-ω5. This work contributes to understanding the non-coding RNA landscape in the PRRSV-swine model and suggests circRNAs as potential targets for future antiviral strategies. Full article

Feline coronaviruses (FCoVs) are divided into two groups: feline infectious peritonitis virus (FIPV) and feline enteric coronavirus (FECV). FIPV is responsible for the severe disease known as feline infectious peritonitis, while FECV typically causes mild symptoms, such as diarrhea, and often does not lead to any disease at all. Currently, it is not possible to distinguish between FIPV and FECV at the molecular level. Therefore, there is an urgent need to understand the molecular features of FIPV. Here, we generated a recombinant virus by replacing the ORF1ab region and the coding sequence for the spike (S) protein of an FECV with the corresponding sequences from FIPVs. The recombinant virus (recFECV-S_DF-2-1ab_FIPV) exhibited similar growth kinetics to its parental strain. Our analysis revealed that the replacement of the ORF1ab in the FECV caused significant alterations in protein expression within the host cells. Furthermore, the presence of the ORF1ab from the FIPV strain resulted in enhanced suppression of the innate immune response compared to the parental strain, as determined through proteomic and transcriptomic studies. Additionally, we demonstrated that the papain-like protease 2 (PL2^pro) of the non-structural protein 3 (NSP3) from both FIPV and FECV functions in immune suppression, and the protease activity is required for this function. Full article

Lumpy skin disease (LSD) is an invasive infectious disease caused by the lumpy skin disease virus (LSDV), which is detrimental to the production of cattle. LSDV encodes about 156 proteins, most of whose functions are still unknown. In this study, we found that the ORF137 protein was identified as one of the strongest inhibitors of IFN-β and ISG expression, determining LSDV ORF137 as a negative regulator of interferon (IFN) β signaling. Further evidence suggests that ORF137 interacts with the signal transduction factor IRF3 and inhibits the activation of IFN-β signaling by reducing Phospho-IRF3 (p-IRF3). Further investigation indicated that overexpression of ORF137 in BMEC could significantly inhibit the transcription of IFN-β and ISGs, thereby promoting the replication of LSDV. More importantly, through homologous recombination, we deleted the ORF137 gene from the LSDV/FJ/CHA/2021 strain and constructed the recombinant strain LSDV-ΔORF137-EGFP. Compared with the parental strain, LSDV-ΔORF137-EGFP showed a weakened effect on inhibiting the transcription of IFN-β and ISGs and a reduced replication level in infected MDBK cells. In summary, ORF137 facilitates LSDV replication by targeting IRF3 to inhibit IFN-β signaling. Our findings reveal a new mechanism by which LSDV suppresses the host antiviral response, which may facilitate the development of attenuated live vaccines for LSDV. Full article

Parkinson’s disease (PD), the second most common neurodegenerative disorder globally, has a notably high prevalence in Sweden (136/10⁵). Although monogenic forms represent only a small subset of PD cases, several genetic factors—including nucleotide repeat expansions (NREs) in ATXN2, ATXN3, C9ORF72, TBP, POLG, TOMM40, CACNA1A, and PRNP—have been implicated in neurodegenerative conditions with parkinsonian features. However, their contribution to PD pathogenesis in the Swedish population remains understudied. We analyzed DNA from 161 Swedish PD patients and 546 controls and evaluated clinical and CSF biomarkers (tau, phospho-tau, and β-amyloid). Intermediate ATXN2 CAG expansions were significantly associated with PD (3.40%, p = 0.0027), and novel promoter structural variations were identified. C9ORF72 G4C2 expansions were also linked to PD (2.48%, p = 0.0018), with distinct methylation patterns in PD cases. POLG Not-10/Not-11Q alleles were positively associated (9.62%, p = 0.014), while TOMM40 showed partial associations for rare genotypes (14.28%, p = 0.0014). Pathological expansions in TBP were marginally significant, while ATXN3, CACNA1A, and PRNP showed no associations. Two-way ANOVA identified significant interactions between APOE E3/E4 and POLG 10/11Q genotypes, affecting age at diagnosis (p = 0.025) and CSF β-amyloid levels. Regression highlighted tau as a key predictor of age at diagnosis (p = 0.02). Longitudinally, APOE E4 predicted cognitive decline (p = 0.015), and TOMM40 haplotypes correlated with motor deficits. In conclusion, ATXN2, C9ORF72, and POLG emerge as key genetic risk factors for PD in the Swedish population, with TOMM40 and TBP contributing partially. Altered CSF biomarker patterns support the existence of distinct molecular subtypes and warrant further investigation of novel ATXN2 variants as potential PD modifiers. Full article

Background: Forsythia suspensa (Thunb.) Vahl is a perennial deciduous shrub of the Oleaceae family. Its dried mature fruits are used as medicine and hold an important position in traditional Chinese medicine. Tyrosine decarboxylase (TyDC) is a key enzyme involved in the synthesis of dopamine in Forsythia suspensa. At the same time, it also affects the growth and development of this species under biotic stress. Methods: This study examined the expression and function of FsTyDC1 under drought and salt stress. The TyDC gene identified in F. suspensa, termed FsTyDC1, has an open reading frame (ORF) of 1518 bp. Results: qRT-PCR and subcellular localization analyses indicated that FsTyDC1 is highly expressed in F. suspensa fruit and its protein is located in the cytoplasm. The gene was silenced using a pTRV2-FsPDS/FsTyDC1 vector with virus-induced gene silencing. Following exposure to drought and salt stress, the leaves of FsTyDC1-silenced plants exhibited increased curling and wilting. Conclusions: The results indicate that FsTyDC1 responds to both salt and drought stress, which provides a foundation for further investigation into the function of FsTyDC1. Full article

Porcine adenovirus serotype 5 (PAdV-5) is an emerging viral vector platform for veterinary vaccines; however, its genomic plasticity and essential replication elements remain incompletely characterized. This study reports the isolation and reverse genetic manipulation of a novel PAdV-5 strain (GD84) from diarrheic piglets in China. PCR screening of 167 clinical samples revealed a PAdV-5 detection rate of 38.3% (64/167), with successful isolation on ST cells after three blind passages. The complete GD84 genome is 32,620 bp in length and exhibited 99.0% nucleotide identity to the contemporary strain Ino5, but only 97.0% to the prototype HNF-70. It features an atypical GC content of 51.0% and divergent structural genes—most notably the hexon gene (89% identity to HNF-70)—suggesting altered immunogenicity. Using Red/ET recombineering, we established a rapid (less than 3 weeks) reverse genetics platform and generated four E3-modified recombinants: ΔE3-All-eGFP, ΔE3-12.5K-eGFP, ΔE3-12.5K+ORF4-eGFP, and E3-Insert-eGFP. Crucially, the ΔE3-All-eGFP construct (complete E3 deletion) failed to be rescued, while constructs preserving the 12.5K open reading frame (ORF) yielded replication-competent viruses with sustained eGFP expression over three serial passages and titers over 10^7.0 TCID₅₀/mL. Fluorescence intensity was inversely correlated with genome size, as the full-length E3-Insert-eGFP virus showed reduced expression compared with the ΔE3 variants. Our work identifies the 12.5K ORF as essential for PAdV-5 replication and provides an optimized vaccine engineering platform that balances genomic payload capacity with replicative fitness. Full article

(1) Background: Hepatitis E (HE) is a novel zoonotic disease caused by hepatitis E virus (HEV). In particular, swine hepatitis E virus (SHEV) genotype IV is one of the main genotypes that infect humans. Open reading frame 3 (ORF3) is an important virulence protein of SHEV, which is involved in virus assembly, release, and regulation of host cell signaling pathways. Circular RNAs (circRNAs), as a type of competitive endogenous RNA (ceRNA), have a closed-loop structure and are special non-coding RNA molecules. They participates in the regulation of multiple biological processes by adsorbing microRNAs (miRNAs). Riboflavin, also known as vitamin B2, is a component of the coenzyme of flavoenzymes in the body. When there is a deficiency of riboflavin, it will affect the biological oxidation process of the host, leading to metabolic disorders. In addition, riboflavin can also affect the synthesis, transportation and decomposition of lipids in the body. It mainly maintains the normal transportation process of fat in the liver. Therefore, the deficiency of riboflavin will lead to the disorder of lipid metabolism in the body. Thus, viral hepatitis is closely related to riboflavin metabolism. However, there are very few reports on SHEV ORF3 affecting the riboflavin metabolism of target cells and thereby influencing viral infection. Therefore, this study investigates this highly significant scientific issue. (2) Methods: In the previous research of our group, adenovirus was used to mediate the overexpression of SHEV ORF3 genotype IV in HepG2 cells. Total RNA was extracted for high-throughput sequencing of circRNAs and transcriptome. KEGG functional enrichment analysis was performed on the data to identify the differentially expressed circRNAs and miRNAs after SHEV infection, and the relevant circRNA-miRNA network in the riboflavin metabolism pathway in HepG2 cells was found. (3) Results: We identified 4 circRNAs in the riboflavin metabolism pathway of HepG2 cells expressing the ORF3 protein of SHEV genotype IV and successfully found 26 relevant circRNA-miRNA networks. (4) Conclusion: We successfully screened and identified circRNAs related to riboflavin metabolism, further identifying the circRNA-miRNA network and its functional targets. For the first time, we investigated the key mechanism by which ORF3 protein influences riboflavin metabolic pathways in target cells through circRNAs, preliminarily revealing that ariboflavinosis can lead to lipid metabolic disorder in the organism. This indicates a close association between viral HE and riboflavin metabolism. Full article

Anelloviruses have a broad mammalian host range, including Torque teno felis virus (FcTTV), a felid-associated member that remains undercharacterized. This is the first comprehensive study of FcTTV in domestic cats in Central Asia. We analyzed blood samples from 206 domestic cats from the large city of Astana, Kazakhstan, collected in 2023–2024. Using nested PCR we identified 63 FcTTV-positive samples (30.6% prevalence), and the sequences were compared to global reference strains. Potential demographic associations (sex and age) were assessed. The study revealed an overall FcTTV prevalence of 30.6%. Infection rates showed no significant sex-related differences: ages varied 4–168 months. ORF1 sequencing revealed multiple FcTTV variants in 27% of samples, with no demographic links. Phylogenetic analysis revealed distinct patterns at both nucleotide and amino acid levels: 3 groups of nucleotide sequences (max divergence 21.68%; intra-cluster 5.15–6.8%), and 3 clusters of amino acid sequences (max divergence 16.81%; intra-cluster 2.82–6.68%). Deletions were found in ORF1 in some variants. Global phylogeny aligned clusters with Asian/European strains (90–98% identity), confirming FcTTV1 affiliation and inter-regional transmission. Our study of FcTTV in Kazakhstan reveals moderate virus prevalence with considerable genetic diversity across viral strains and frequent co-infections with multiple variants. Full article

Hepatitis E virus (HEV) is an emerging zoonotic pathogen, with swine identified as a major reservoir. Despite the global significance of HEV, epidemiological data regarding its presence in Greek pig farms remain limited. This study investigated the presence of HEV RNA in swine populations across Greece. In 2019, a total of 280 fecal samples from finishing pigs were collected from 28 pig farms in diverse geographic regions. Pooled samples were analyzed by real-time RT-PCR targeting the conserved ORF3 region of the HEV genome (without genotyping). HEV RNA was detected in 42.9% (12/28) of farms, with positive farms identified in five of the six surveyed regions, suggesting widespread viral circulation. These findings confirm, for the first time, the presence of HEV in the Greek swine population, while the observed prevalence aligns with intermediate to high levels reported in other European countries. Considering the zoonotic potential of HEV, especially via occupational exposure or consumption of contaminated pork products, these results highlight the need for continued surveillance and further investigation into potential public health implications. Full article

Human noroviruses (HuNoVs) stand as the primary cause of acute viral gastroenteritis outbreaks worldwide, particularly impacting children under the age of five. In Russia, reports of norovirus gastroenteritis have surged, especially in the post-COVID-19 era starting in 2022, with elevated infection rates reported into 2024. These viruses exhibit significant mutational variability, leading to the emergence of recombinant strains that can evade immune responses. A comprehensive examination of the complete genome is crucial for understanding the evolution of norovirus genes and for predicting potential outbreaks. This research focuses on analyzing the genotypic composition of HuNoVs circulating in the Sverdlovsk region during 2024, using Sanger sequencing and next-generation sequencing (NGS). Biological samples were collected (n = 384) from patients diagnosed with norovirus infection within the region. Bioinformatics analysis targeted the nucleotide sequences of the ORF1/ORF2 fragment and the assembly of complete genomes for the GII.4 and GII.7 genotypes. In total, 220 HuNoVs were characterized, representing 57.3% of the collected samples. The main capsid variants forming the predominant genotypic profile included GII.4 (n = 88, 40%), GII.7 (n = 86, 39%), and GII.17 (n = 14, 6%). Using NGS, we successfully assembled 8 out of 10 complete genomes for noroviruses GII.4[P16] and GII.7[P7]. Non-synonymous substitutions appeared at amino acid sites corresponding to the subdomains of VP1 in these strains. This molecular–genetic analysis provides contemporary insights into the genotypic composition, circulation patterns, and evolutionary dynamics associated with the dominant genovariants GII.4[P16] and GII.7[P7]. Full article

Macrophomina phaseolina is a widely distributed soilborne phytopathogenic fungus that causes destructive diseases such as charcoal rot and stem canker, posing serious threats to crop yield and quality. In recent years, mycoviruses have gained attention as potential biological control agents. In this study, a novel double-stranded RNA (dsRNA) virus was identified from M. phaseolina strain 22C-8, isolated from sesame (Sesamum indicum L.) charcoal rot samples in Fuyang, Anhui Province, China. The viral genome comprised four dsRNA segments, each encoding a single open reading frame (ORF) predicted to encode RNA-dependent RNA polymerase (RdRp), coat protein (CP), and two hypothetical proteins. Phylogenetic analysis classified the virus as a new member of the genus Betachrysovirus in the family Chrysoviridae, and it was designated Macrophomina phaseolina chrysovirus 2 (MpChrV2). Pathogenicity assays in sesame seedlings revealed that MpChrV2 infection significantly reduced the virulence of M. phaseolina strain 22C-8. In contrast, virus-free derivatives (22C-8-VF18), obtained via protoplast regeneration, caused more severe symptoms and exhibited enhanced growth rates, indicating that MpChrV2 alters fungal physiology and pathogenicity. These findings suggest that MpChrV2 possesses a typical hypovirulence phenotype and holds promise as a biocontrol agent for sesame charcoal rot. Full article