Search Results (626)

Various SARS-CoV-2 remdesivir resistance-associated substitutions (RAS) have been reported, but a comprehensive comparison of their resistance levels is lacking. We identified novel RAS and performed head-to-head comparisons with known RAS in Vero E6 cells. A remdesivir escape polyclonal virus exhibited a 3.6-fold increase in remdesivir EC₅₀ and mutations throughout the genome, including substitutions in nsp12 (E796D) and nsp14 (A255S). However, in reverse-genetics infectious assays, viruses harboring both these substitutions exhibited only a slight decrease in remdesivir susceptibility (1.3-fold increase in EC₅₀). The nsp12-E796D substitution did not impair viral fitness (Vero E6 cells or Syrian hamsters) and was reported in a remdesivir-treated COVID-19 patient. In replication assays, a subgenomic replicon containing nsp12-E796D+nsp14-A255S led to a 16.1-fold increase in replication under remdesivir treatment. A comparison with known RAS showed that S759A, located in the active site of nsp12, conferred the highest remdesivir resistance (106.1-fold increase in replication). Nsp12-RAS V166A/L, V792I, E796D or C799F, all adjacent to the active site, caused intermediate resistance (2.0- to 11.5-fold), whereas N198S, D484Y, or E802D, located farther from the active site, showed no resistance (≤2.0-fold). In conclusion, our classification system, correlating replication under remdesivir treatment with RAS location in nsp12, shows that most nsp12-RAS cause moderate resistance. Full article

Cowpea (Vigna unguiculata [L.] Walp) is a vital food security crop in sub-Saharan Africa, including Eswatini. The productivity of the crop is low (<600 kg/ha) in the country due to a lack of improved, locally adapted, and farmer-preferred varieties with biotic and abiotic stress tolerance. The objective of the study was to assess the agronomic performance of newly developed elite cowpea mutants to select best-yielding and adapted pure lines for production and genetic improvement in Eswatini. A total of 30 cowpea genotypes, including 24 newly developed advanced mutant lines, their 3 founder parents and 3 local checks, were profiled for major agronomic traits in two selected sites (Lowveld Experiment and Malkerns Research Stations) using a 6 × 5 alpha lattice design with three replications. A combined analysis of variance revealed that the genotype x location interaction effects were significant (p < 0.05) for germination percentage (DG %), days to flowering (DTF), days to maturity (DMT), number of pods per plant (NPP), pod length (PDL), number of seeds per pod (NSP), hundred seed weight (HSW), and grain yield (GYD). Elite mutant genotypes, including NKL9P7, BRR4P11, SHR9P5, and NKL9P7-2 exhibited higher grain yields at 3158.8 kg/ha, 2651.6 kg/ha, 2627.5 kg/ha, and 2255.8 kg/ha in that order. The highest-yielding mutant, NKL9P7, produced 70%, 61%, and 54% more grain yield than the check varieties Mtilane, Black Eye, and Accession 792, respectively. Furthermore, the selected genotypes displayed promising yield components such as better PDL (varying from 13.1 to 26.3 cm), NPP (15.9 to 26.8), and NSP (9.8 to 16.2). Grain yield had significant positive correlations (p < 0.05) with DG %, NSP, and NPP. The principal component analysis (PCA) revealed that 81.5% of the total genotypic variation was attributable to the assessed quantitative traits. Principal component (PC) 1 accounted for 48.6%, while PC 2 and PC 3 contributed 18.9% and 14% of the overall variation, respectively. Key traits correlated with PC1 were NPP with a loading score of 0.91, NSP (0.83), PDL (0.73), GYD (0.68), HSW (0.58), DMT (−0.60), and DTF (−0.43) in a desirable direction. In conclusion, genotypes NKL9P7, BRR4P11, SHR9P5, NKL9P7-2, Bira, SHR3P4, and SHR2P7 were identified as complementary parents with relatively best yields and local adaptation, making them ideal selections for direct production or breeding. The following traits, NPP, NSP, PDL, GYD, and HSW, offered unique opportunities for genotype selection in the cowpea breeding program in Eswatini. Full article

Coronaviruses, particularly those classified as highly pathogenic species, pose a significant threat to global health. These viruses hijack host cellular membranes and proteins to facilitate their replication, primarily through the formation of replication organelles (ROs). However, the precise regulatory mechanisms underlying RO formation remain poorly understood. To elucidate these mechanisms, we conducted mass spectrometry analyses, identifying interactions between the host protein DnaJ homolog subfamily C member 11 (DNAJC11) and the SARS-CoV-2 nonstructural protein 3 (NSP3) protein. Notably, results showed that DNAJC11 depletion reduces SARS-CoV-2 infection, indicating possible positive regulatory involvement. But the ectopic expression of DNAJC11 did not lead to marked alterations in immune or inflammatory responses. DNAJC11 enhanced NSP3 expression stability through endogenous apoptosis pathways and facilitated its interaction with NSP4, thereby promoting the formation of double-membrane vesicles (DMVs). Knockdown of DNAJC11 reduced DMV number and size, accompanied by dysregulation of the endoplasmic reticulum and mitochondria. However, supplementation with DNAJC11 restored both DMV number and size. These findings provide novel insights into the role of DNAJC11 as a host factor that modulates DMV formation and supports SARS-CoV-2 replication by targeting the NSP3 protein. This study advances our understanding of the molecular interactions between host and viral components and highlights DNAJC11 as a potential target for antiviral interventions. Full article

Rye (Secale cereale L.) is one of the most important cereals cultivated in Central and Eastern Europe, valued for its high resistance to environmental stress and high levels of bioactive compounds, such as dietary fiber (DF) and alkylresorcinols (ARR). The aim of the study was to evaluate the content and variability of DF fractions and ARR in rye grain of hybrid and population cultivars. The research was conducted on grain from four rye cultivars cultivated in five locations over three consecutive growing seasons. The content of DF, its fractions, and ARR, was determined using enzymatic–gravimetric and colorimetric methods. The results showed significant variability in all analyzed traits, with environmental conditions and G×E interaction having the greatest impact on their content. Hybrid cultivars were characterized by a higher and more stable content of bioactive compounds. Notable average values for hybrids vs. populations included DF: 153.9 vs. 151.7 g kg⁻¹, NSP: 129.4 vs. 127.7 g kg⁻¹, lignin: 24.5 vs. 24.0 g kg⁻¹, β-glucan: 21.7 vs. 20.6 g kg⁻¹, and ARR: 1015 vs. 987 g kg⁻¹. The KWS Serafino cultivar characterized by the highest and most stable content of bioactive compounds. Selecting genotypes with stable chemical profiles regardless of environmental conditions is crucial for developing nutritionally valuable rye-based products. Full article

Chikungunya virus (CHIKV), a mosquito-borne alphavirus, has re-emerged, causing widespread outbreaks and a significant clinical burden. Despite advances in virology, the molecular mechanisms governing CHIKV’s interaction with host cells remain poorly understood. In this study, we aimed to identify novel host protein interactors of the CHIKV nonstructural protein 3 (nsP3), a critical component of the viral replication complex, using mass spectrometry-based proteomic profiling in liver-derived Huh7 cells. Co-immunoprecipitation followed by LC-MS/MS identified a wide array of host proteins associated with nsP3, revealing 52 proteins classified as high-confidence (FDR of 1%, and unique peptides > 2) CHIKV-specific interactors. A bioinformatic analysis using STRING and Cytoscape uncovered interaction networks enriched in metabolic processes, RNA processing, translation regulation, cellular detoxification, stress responses, and immune signaling pathways. A subcellular localization analysis showed that many interactors reside in the cytosol, while others localize to the nucleus, nucleolus, and mitochondria. Selected novel host protein interactions were validated through co-immunoprecipitation and immunofluorescence assays. Our findings provide new insights into the host cellular pathways hijacked by CHIKV and highlight potential targets for therapeutic intervention. This is the first report mapping direct nsP3–host protein interactions in Huh7 cells during CHIKV infection. Full article

Aboriginal and Torres Strait Islander people who inject drugs face persistent health inequities, highlighting the need for programs that meet the needs of these groups. This study explored how intersectional stigma and discrimination affect Aboriginal and Torres Strait Islander people’s access to quality healthcare. Aboriginal and Torres Strait Islander participants aged ≥18 years who had injected drugs within the past 12 months were recruited from two regional needle and syringe programs (NSPs) and a major city NSP in Queensland, Australia. Participants completed a structured survey and yarned with an Aboriginal researcher and non-Indigenous research assistant about their healthcare experiences. Through a process of reflexive and thematic analysis, three major qualitative themes emerged: participants’ social circumstances and mental health challenges made help-seeking difficult and complex; enacted stigma and racism diminished access to health services and the quality of care received; and injecting drug use was associated with disconnection from culture and community. Privileging the expertise and voices of those with lived/living experience is essential for the creation of culturally safe, inclusive, and destigmatising healthcare services for Aboriginal and Torres Strait Islander people who inject drugs. Full article

Coronavirus non-structural protein 1 (nsp1) is a pathogenic determinant of Betacoronaviruses. Previous studies demonstrated that the nsp1 of various coronaviruses induces host shutoff through a variety of mechanisms; however, there is little information on the function of bovine coronavirus (BCoV) nsp1. We aimed to characterize the host gene expression suppression function of BCoV nsp1. We first confirmed that the expression of BCoV nsp1 in MAC-T cells, a bovine mammary epithelial cell line, suppressed host and reporter gene expression. Subsequently, lysine and phenylalanine at amino acid positions 232 and 233, respectively, were identified as key residues required for this suppressive effect. Expression levels of housekeeping genes are comparable in cells expressing wild-type BCoV nsp1 and a mutant with alanine substitutions at positions 232 and 233 (BCoV nsp1-KF). Wild-type BCoV nsp1 localized to both the cytoplasm and nucleus; however, BCoV nsp1-KF exhibited prominent nuclear accumulation with dot-like structures. Using confocal microscopy and co-sedimentation analysis, we identified an association between wild-type BCoV nsp1, but not BCoV nsp1-KF, and ribosomes, suggesting that ribosome binding is required for BCoV nsp1-mediated suppression of host gene expression. This is the first study of the characterization of host gene expression suppression by BCoV nsp1. Full article

PRRSV continues to evolve, complicating its epidemiological landscape in China. In this study, we isolated a novel PRRSV strain, GZ2022, from a swine farm in Guizhou Province. Subsequent analyses performed on this isolate included complete genome sequencing, phylogenetic analysis, recombination assessment, and characterization of its biological properties. Phylogenetic analysis revealed that GZ2022 clusters within Lineage 1 (NADC30-like) and features a 131-amino-acid deletion in NSP2, consistent with NADC30-derived strains. Recombination analysis identified NADC30 as the major parental strain (75% genomic contribution), with a minor recombinant region (25%) derived from the highly pathogenic HuN4 strain. In vitro growth kinetics revealed peak viral titers in Marc-145 cells at 72 h post infection (hpi). Pathogenicity was evaluated in 21-day-old piglets infected with GZ2022, the highly pathogenic PRRSV strain WUH3, or negative controls. Both infected groups exhibited typical PRRS clinical signs (fever, respiratory distress) and histopathological lesions (interstitial pneumonia, pulmonary consolidation). However, GZ2022-infected piglets exhibited attenuated virulence compared to WUH3, with reduced pulmonary hemorrhage and 0% mortality compared to 80% in the WUH3 group. Seroconversion (N-protein antibodies) was observed at 14 dpi (days post inoculation) in GZ2022-infected animals, persisting throughout the 28-day trial. Viral shedding dynamics aligned with moderate pathogenicity. These findings classify GZ2022 as a moderately virulent NADC30-like recombinant strain with partial HuN4-derived genomic regions. The emergence of such strains underscores the need for sustained surveillance of PRRSV genetic diversity and systematic evaluation of the biological properties of novel variants to refine control measures and inform vaccine development. Full article

Swine acute diarrhea syndrome coronavirus (SADS-CoV), initially identified in China in February 2017, severely impacts the swine industry by causing lethal watery diarrhea in neonatal piglets. Understanding the molecular mechanism employed by SADS-CoV to evade the host’s immune defenses is of utmost importance. In this study, using the porcine ileum epithelial cell line IPI-FX as an in vitro model, we investigated the highly pathogenic SADS-CoV GDS04 strain and its nonstructural protein 5 (nsp5) for their roles in inhibiting interferon-beta (IFN-β) production. Our findings indicated that GDS04 inhibited poly(I:C)-induced IFN-β production by impeding the promoter activities of IRF3 and NF-κB. As a 3C-like protease, SADS-CoV nsp5 functioned as an interferon inhibitor by interacting with IKKε, reducing its protein abundance, and inhibiting its phosphorylation. This study enhances our understanding of the interaction between coronaviruses and their hosts, providing novel insights into the evasion of the immune system by coronaviruses. Full article

The demand for secure communication in the age of quantum technologies has driven progress in quantum key distribution (QKD) techniques for optical networks. This research addresses the issues of high blocking probabilities (BPs) and the proper utilization of quantum resources in varying network loads by introducing a novel heuristic approach, termed dynamic security-aware quantum resource allocation (D-SQRA), designed for dynamic resource allocation in QKD-enabled optical networks. We propose two D-SQRA algorithms to employ an adaptive resource assignment (RA) strategy that concurrently addresses routing, wavelength, and time-slot selection while dynamically modifying security levels according to the real-time network load and resource availability. We evaluate the proposed D-SQRA performance against two conventional methods, namely, fixed security quantum resource allocation (F-SQRA) and baseline quantum resource allocation (B-QRA). We discuss the results for NSFNET and UBN24 topologies for network security performance metrics such as network security performance (NSP), BP, quantum key utilization (QKU), and time-slot utilization. The results show that the proposed D-SQRA algorithms provide significant improvement with respect to conventional techniques in addressing proper resource utilization and management by reducing BPs of the new incoming connection requests. Full article

Background: Porcine Reproductive and Respiratory Syndrome (PRRS) is a highly contagious disease characterized by reproductive failure in sows and severe respiratory disorders across all swine ages, causing significant economic losses. In China, the PRRSV epidemiological landscape is complex, with the coexistence of multiple lineages and frequent recombination. The major circulating strains include sublineages 1.8 (NADC30-like PRRSV) and 1.5 (NADC34-like PRRSV), along with lineages 8 (HP-like PRRSV) and 5 (VR2332-like PRRSV), highlighting the urgent need for rapid detection and lineage differentiation. Methods: A quadruplex RT-qPCR assay was developed targeting lineage-specific deletions in the NSP2 gene to simultaneously detect PRRSV-2 and differentiate NADC30-like PRRSV, HP-like PRRSV, and NADC34-like PRRSV strains. The assay was optimized with respect to reaction conditions, including annealing temperature, primers, and probe concentrations. The method’s performance was evaluated in terms of specificity, sensitivity, repeatability, stability, limit of detection (LOD), and consistency with sequencing results. Results: The assay demonstrated high sensitivity (LOD of 3 copies/μL), high specificity, and good repeatability (coefficient of variation < 1.5%). Field application using 938 samples from Guangxi A and B farms revealed NADC30-like PRRSV wild-type strains at positivity rates of 13.44% and 3.53%, respectively. Positive samples selected for sequencing were further confirmed using ORF5-based phylogenetic analysis and NSP2 deletion pattern comparison, which aligned with RT-qPCR detection results. Field application primarily detected NADC30-like PRRSV, while further validation is still needed for HP-like and NADC34-like strains. The developed quadruplex RT-qPCR assay enables rapid and simultaneous detection of PRRSV-2 and differentiation of three major lineages, providing a sensitive, specific, and reliable tool for distinguishing vaccine-derived from circulating strains and supporting targeted disease surveillance and control in swine farms. Full article

This study aims to explore how the macro-geopolitical economic cooperation policy is connected with student mobility in higher education at the micro level. Since the internationalization of higher education and student mobility, which mainly occurred in universities at the institutional level, the relationship between macro governmental goals and economic strategies tends to be less emphasized. Also, the factors influencing student mobility focus more on their characteristics. Therefore, this study investigates how student mobility in higher education has been changed according to the New Southern Policy (NSP) in South Korea, especially focusing on the policy targeted in ASEAN regions. Also, we describe trends of student mobility according to different characteristics of a university under the policy. The findings of this study indicate that when formulating and implementing policy, it is imperative to acknowledge the limitations of a macro-level, strategic approach, even when considering a multitude of factors. Furthermore, this study suggests that macroeconomic policies may exert unanticipated impacts on areas that have not been explicitly addressed. Full article

Foot-and-mouth disease (FMD) is a contagious transboundary animal disease that causes economic loss and obstacles to international trade. Frequent FMD outbreaks in Cambodia negatively impact farmers’ and smallholders’ incomes. This study aimed to estimate the seroprevalence of FMD Non-Structural Protein (NSP) antibodies, which are an indicator of FMD antibodies raised during a natural infection rather than those produced following vaccination, that were detected using a commercial enzyme-linked immunosorbent assay (ELISA). Sample collection from cattle and pigs (n = 2238) was performed at ten abattoirs in seven provinces between October 2019 and December 2020. Overall seroprevalence in cattle and pigs was 43.2% (363/839; 95% CI 39.8–46.7), and 0.6% (9/1399; 95% CI 0.2–1.2), respectively. Only the cattle dataset was included in the risk factor analysis, as the prevalence of sero-reactors was too low in the pig dataset to be analyzed. Significant risk factors identified by the logistic regression model included the province of origin (p = 0.02), body condition score (BCS) (p = 0.0002) and sex (p = 0.0007). Odds ratios of the significant risk factors were 7.05 (95% CI 1.43–34.67; p = 0.02) for cattle that originated from Kampong Thom, 1.41 (95% CI 1.05–1.89; p = 0.02) for female cattle, and 3.28 (95% CI 1.06–10.12; p = 0.04) for animals with BCS of 3/5. The study revealed that the seroprevalence of FMD NSP in cattle presented at the abattoirs was high, while the FMD NSP seroprevalence in abattoir pigs was very low. Further investigation is required to map the disease distribution in Cambodia, especially the serotypes and strains causing clinical disease. These findings call for the extension of work on effective disease prevention measures. Full article

In Cali, Colombia, 405,689 COVID-19 cases were reported until March 2023, with 2463 complete genome sequences available for analysis. SARS-CoV-2 genomic data from Cali were analyzed to determine the prevalence of variants as well as the mutation frequencies. This study identified Nextstrain clades, Pango lineages, and specific mutations in key viral proteins. A total of 23 Nextstrain clades and 118 Pango lineages were detected, including variants of interest (Lambda, Mu) and variants of concern (Alpha, Gamma, Delta, Omicron). Analysis identified 2424 missense mutations, with notable frequencies in NSP3 (465), S (367), NSP2 (205), N (180), ORF3a (144), NSP12b (113), and NSP13 (108). The study also observed a high prevalence of simultaneous transmission of multiple variants. The COVID-19 epidemic waves in Cali were shaped more by social and economic dynamics than by the emergence of specific SARS-CoV-2 variants. These findings highlight the importance of context-specific public health interventions to mitigate future outbreaks effectively. Full article

Due to its high genomic variability, the epidemiological landscape of porcine reproductive and respiratory syndrome virus (PRRSV) has become increasingly complex in recent years. From 2022 to 2023, we collected a total of 1044 clinical samples from pigs suspected of PRRSV infection in China and discovered a PRRSV-positive rate of 29.8% (311/1044) using RT-PCR targeting the nsp2 gene. Among these positive samples, NADC30/34-like PRRSV, highly pathogenic PRRSV (HP-PRRSV), and classical PRRSV strains accounted for 60.1%, 37.9%, and 4.5%, respectively. These results indicate that the most prevalent PRRSV strains in China are NADC30/34-like PRRSV, followed by HP-PRRSV. Two PRRSV strains, JX03 and HN08, were isolated, and TCID₅₀ assays were performed to determine their titers at different time points post-infection, revealing differences in their proliferation kinetics. Phylogenetic, amino acid sequence, and recombination analyses demonstrated that the JX03 and HN08 strains cluster within lineage 8 (HP-PRRSV) and sublineage 1.5 (NADC34-like PRRSV), respectively. Notably, the HN08 strain was identified as a recombinant between the NADC30-like and NADC34-like strains, while no recombination event was detected in the JX03 strain. Pathogenicity assessments showed that the JX03 strain exhibited higher pathogenicity than the CHN-HB-2018 strain (a NADC30-like PRRSV strain was previously isolated by our lab), as evidenced by differences in clinical signs and mortality rates in piglets. In contrast, HN08 displayed no obvious clinical symptoms or mortality, revealing lower pathogenicity than the CHN-HB-2018 strain. These findings provide valuable information on the epidemiological and genetic characteristics of PRRSV strains in China, laying a foundation for the development of effective strategies against PRRSV. Full article