Search Results (58)

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

Cross-ecosystem transmission of plant pathogens from crops to natural forests is increasingly recognized as a key factor in disease emergence and biodiversity loss. Agricultural systems serve as major sources of inoculum, with landscape interfaces—such as crop–forest edges, riparian zones, abandoned orchards, and nursery–wildland transitions—acting as active epidemiological gateways. Biological vectors, abiotic dispersal, and human activities collectively enable pathogen movement across these boundaries. Host-range expansion, recombination, and hybridization allow pathogens to infect both cultivated and wild hosts, leading to generalist and recombinant lineages that survive across diverse habitats. In natural ecosystems, such introductions can alter community composition, decrease resilience, and intensify the impacts of climate-driven stress. Advances in molecular diagnostics, genomic surveillance, environmental DNA, and remote sensing–GIS (Geographic Information System) approaches now enable high-resolution detection of pathogen flow across landscapes. Incorporating these tools into interface-focused monitoring frameworks offers a pathway to earlier detection, better risk assessment, and more effective mitigation. A One Health, landscape-based approach that treats agro–wild interfaces as key control points is essential for reducing spillover risk and safeguarding both agricultural productivity and the health of natural forest ecosystems. Full article

Modern agricultural operations generate high-volume and diverse data (historical and stream) from various sources, including IoT devices, robots, and drones. This paper presents a novel smart farming architecture specifically designed to efficiently manage and process this complex data landscape.The proposed architecture comprises five distinct, interconnected layers: The Source Layer, the Ingestion Layer, the Batch Layer, the Speed Layer, and the Governance Layer. The Source Layer serves as the unified entry point, accommodating structured, spatial, and image data from sensors, Drones, and ROS-equipped robots. The Ingestion Layer uses a hybrid fog/cloud architecture with Kafka for real-time streams and for batch processing of historical data. Data is then segregated for processing: The cloud-deployed Batch Layer employs a Hadoop cluster, Spark, Hive, and Drill for large-scale historical analysis, while the Speed Layer utilizes Geoflink and PostGIS for low-latency, real-time geovisualization. Finally, the Governance Layer guarantees data quality, lineage, and organization across all components using Open Metadata. This layered, hybrid approach provides a scalable and resilient framework capable of transforming raw agricultural data into timely, actionable insights, addressing the critical need for advanced data management in smart farming. Full article

The GI.3 norovirus is the most detected and recombinant-rich genotype within genogroup I, yet the mechanistic basis for its epidemiological success remains poorly understood. This study integrates Bayesian evolutionary analysis with in vitro enzymology to investigate the link between RdRp function and the evolutionary dynamics of GI.3 NoV. We analyzed 831 GI.3 sequences, finding that prevalent strains (GI.3[P3] and GI.3[P13]) exhibited significantly higher evolutionary rates in both the RdRp and VP1 genes than non-prevalent strains (GI.3[P10] and GI.3[P14]). While the RdRp gene displayed a strong molecular clock signal, the VP1 gene’s evolution was more complex, showing cluster-specific trends. Functionally, the RdRps from prevalent strains demonstrated superior enzymatic activity and substrate affinity (K_m: GI.3[P13] = 0.092 mM; GI.3[P3] = 0.176 mM) compared to non-prevalent strains (K_m: GI.3[P14] = 0.273 mM). Notably, GI.3 RdRp required higher manganese ion concentrations for optimal activity than previously reported for GII strains, suggesting a potential biochemical constraint. Our findings demonstrate a clear correlation between RdRp enzymatic efficiency, evolutionary rate, and strain prevalence. We propose that a highly active RdRp may potentially accelerate VP1 evolution and confer a replicative advantage, underpinning the dominance of specific GI.3 lineages. This work provides crucial experimental evidence linking viral polymerase function to evolutionary and epidemiological outcomes. Full article

Japanese encephalitis virus (JEV) is a mosquito-borne zoonotic flavivirus causing severe neurological disease across Asia, and genotype V (GV) is now predominant in Korea. Despite frequent detection of GV in mosquitoes, human-derived complete genome data remain scarce. To elucidate the molecular and antigenic characteristics of human GV infections, cerebrospinal fluid samples from unvaccinated patients positive for JEV RNA during 2018–2023 were subjected to virus isolation in LLC-MK2 cells (rhesus monkey kidney-derived epithelial cell line). Three human GV isolates (K18P80, K23P84, K23P88) were successfully obtained and their complete open reading frames (~10.3 kb) sequenced. Phylogenetic analysis with representative JEV strains (GI–GV) revealed that these isolates form a distinct lineage, clustering into two domestic clades (Clade I and II), suggesting endemic circulation and local evolution in Korea. Sequence identities with GIII-based vaccine strains were low (79% nucleotide, 91.1% amino acid), with notable divergence in nonstructural regions. Three consistent E protein substitutions (Q52E, S156T, D292E) near antigenic epitopes indicate possible immune escape. Additional clade-defining substitutions in NS3 (L31F) and NS5 (K269R, M330I) were shared with mosquito isolates, supporting human–vector molecular continuity. These findings provide fundamental genomic evidence of human JEV GV in Korea and highlight the need for genotype-specific surveillance and next-generation vaccine evaluation. Full article

As a form of living cultural heritage, local residential landscapes manifest the essence of long-term, resilient human–land interactions. The Wuling Corridor, a vital ethnic and cultural passage connecting the Central Plains with Southwest China in Chinese history, serves as a crucial region for the mixed residence and cultural exchange of Tujia, Miao, Dong, Han, and other ethnic groups. Within this region, Ganlan stands as both the most representative vernacular architectural heritage and a residential form that is still extensively used, constituting a continuous and unique residential landscape. The spatial distribution patterns of Ganlan are the physical witness of the history of ethnic groups adapting to the complex topographic and cultural conditions. Current research focuses on the case description of single Ganlan forms, failing to systematically investigate the spatial formation mechanisms of Ganlan as a residential landscape from a geographical continuum perspective. Therefore, this study establishes a geographical database encompassing 9425 Ganlan samples from the Wuling Corridor. It integrates the geographic information system (GIS) with clustering algorithms to systematically identify the distribution patterns of Ganlan within specific geographic–cultural units and their coupling relationships with natural environments. It conducts quantitative analysis on the key driving factors concerning the emergence and evolution of Ganlan in the study area; the findings reveal the following: (1) Ganlan buildings exhibit a spatially aggregated distribution pattern along major water systems, demonstrating characteristics of multi-ethnic sharing and spatial interweaving. (2) Their distribution is constrained by natural geographical factors and influenced by the transmission pathways of construction techniques during ancient ethnic migrations to the southwest China. (3) Within multi-ethnic settlement structures, inter-ethnic cultural interactions (particularly with Central Plains culture) serve as a key driving force for the typological evolution of Ganlan. (4) The evolutionary lineage of “full-Ganlan,” “semi-Ganlan,” and “courtyard-style Ganlan” systematically demonstrates the dynamic adaptive capacity of local residential systems. Additionally, by integrating massive Ganlan heritage data with multiple spatial analysis methods, the study serves as a typical case study illuminating the adaptive strategies and resilience mechanisms of Ganlan as a local residential landscape formed in response to the environmental conditions and social changes. Also, it provides a scientific basis for the holistic conservation of architectural heritages shared by multiple ethnic groups and the integrated development of local cultural tourism industries. Full article

Background: As infectious bronchitis virus (IBV) strains similar to the IBV S95 live attenuated vaccine strain have been occasionally detected in poultry farms in Japan, we investigated the suspicion that outbreaks of the disease were related to the S95 vaccine. Methods: We isolated ten S95 vaccine-like strains, classified in the JP-I genotype of S1, the VIb (Y-4) genogroup of S2, and the GI-18 lineage, from IBV-affected chickens in Japan between 2020 and 2024. The whole-genome sequence and adaptation to embryonated chicken eggs were investigated. We developed a method for distinguishing the S95 vaccine strain from S95-like wild-type strains using specific primer sets having either the S95 vaccine or S95 parent-specific nucleotide at the 3′ termini of primers on the ORF2 gene. Results: Nine of ten S95 vaccine-like strains lacked identical mutations to the ORF1ab, ORF2, and ORF5a genes that the S95 vaccine strain acquired during attenuation. The remaining S95-like strain, B3389, had identical mutations to the S95 vaccine strain in the ORF1ab and ORF5a genes. The B3389 strain, however, had strain-specific nucleotides that were not found in the S95 vaccine or S95 parent strains, and produced fewer embryonated egg-adapted phenotypes than the S95 vaccine strain. Conclusions: The ten S95-like strains appear not to have emerged from the S95 vaccine strain. Instead, sporadic outbreaks of S95 vaccine-like IBV strains in Japan were indicated. A method for distinguishing and excluding the S95-like wild-type strains as suspected revertants of the S95 vaccine may be utilized for comprehensive IBV surveillance to facilitate development of a vaccination strategy. Full article

Background/Objectives: Developmental biologist Conrad Waddington proposed that evolution is shaped not only by genetic mutations and natural selection but also by environmentally responsive developmental mechanisms. Building on this premise, the epigenetic regulation of three master genes central to mammalian embryogenesis—OCT4, SOX2, and hTERT—focusing on their intragenic CpG islands (iCpGIs), which are crucial for transcriptional control and chromatin state modulation, were investigated. Methods: By performing a phylo-epigenetic comparison across 12 primate species, strong conservation of CpG-rich regions, punctuated by lineage-specific CpG transitions, particularly CpG→TpG and CpG→CpA was identified. Results: These mutational patterns align with methylation-dependent deamination mechanisms and highlight iCpGIs as evolutionarily constrained, epigenetically plastic elements. Notably, CpG variation alone recapitulated known primate phylogenies, suggesting that methylation-sensitive sites within iCpGIs encode both developmental and evolutionary information. Conclusions: It is proposed that such sites are prone to Environmentally Determined Epimutations (EDEMs)—methylation-driven, nutrition-sensitive changes that persist across generations and modulate gene regulatory capacity. This integrative framework advances Waddington’s concept of canalization by providing a molecular mechanism through which environmental factors can reshape developmental trajectories and contribute to evolutionary innovation. Full article

Infectious bronchitis virus (IBV) remains a major threat to poultry health worldwide due to frequent genetic changes mainly driven by recombination and limited cross-protection between genotypes. In this study, we analyzed IBV strains collected from clinical outbreaks in Chile between 1986 and 2021 to assess the long-term impacts of live-attenuated vaccines (Massachusetts and 4/91) on viral evolution. Phylogenetic analysis of the S1 and N genes revealed four major lineages circulating in Chile—GI-1, GI-13, GI-16, and a novel monophyletic clade we propose as GI-31. The latter, identified in isolates from 1986 to 1988, is highly divergent (22–24%) from other known lineages, representing a previously unreported South American IBV variant. Despite widespread Mass vaccination, genetically distinct field strains circulated during the 1980s, facilitating potential recombination with GI-1 vaccine-derived strains, including evidence of shared ancestry with GI-11, an endemic lineage from Brazil. Non-recombinant GI-16, likely introduced from Asia, was detected in isolates from 2009. Notably, a recombinant strain emerged in 2015, four years after 4/91 vaccine introduction, indicating vaccine–field-strain genetic exchange. By 2017, isolates with >99% identity to the 4/91 strain were recovered, suggesting vaccine-derived variants. In 2021, GI-1 re-emerged, showing recombination signatures between GI-1 and GI-13 (4/91-derived) strains, likely reflecting suboptimal or inconsistent vaccination strategies. Selection analyses showed strong purifying selection across most of the S1 gene, with limited sites under positive selection in the receptor-binding domain. Phylodynamic reconstruction revealed time-structured evolution and multiple introduction events over 35 years, with lineage-specific tMRCA estimates. Collectively, these findings highlight the emergence of a novel lineage in South America and demonstrate that vaccine use, while mitigating disease, has significantly shaped the evolution of IBV in Chile. Our results underscore the importance of continuous genomic surveillance to inform vaccine strategies and limit recombinant emergence. Full article

Background: Infectious bronchitis virus (IBV) is a gammacoronavirus that causes a highly contagious disease in chickens and seriously endangers the poultry industry. The GI-19 is a predominant lineage. However, no effective commercially available vaccines against this virus are available. Methods: In this present study, the CHO eukaryotic and the E.coli prokaryotic expression system were used to express S1-SpyTag and AP205-SpyCatcher, respectively. Subsequently, the purified S1-SpyTag and AP205-SpyCatcher were coupled to form the nanoparticles AP205-S1 (nAP205-S1) in PBS buffer at 4 °C for 48 h. S1-SpyTag and nAP205-S1 were formulated into vaccines with white oil adjuvant and employed to immunize 1-day-old SPF chickens for the comparative evaluation of their immune efficacy. Results: The nAP205-S1 vaccine in chickens induced robust IBV-specific humoral and cellular immune responses in vivo. Importantly, the humoral and cellular immune responses elicited by the nAP205-S1 vaccine were more robust than those induced by the IBV S1-SpyTag vaccine at both the same dose and double the dose, with a notably significant difference observed in the cellular immune response. Furthermore, experimental data revealed that chicken flocks vaccinated with nAP205-S1 achieved 100% group protection following a challenge, exhibiting a potent protective immune response and effectively inhibiting viral shedding. Conclusions: These results reveal the potential of developing a novel nanoparticle vaccine with broadly protective immunity against GI-19 IBV. Full article

Infectious bronchitis virus (IBV) is a chicken pathogen present in commercial poultry farms worldwide. It is classified within the species Avian coronavirus, genus Gammacoronavirus. As with other members of the family Coronaviridae, it has a single positive-sense RNA genome with 27.6 Kb and presents viral particles with a typical crown-like aspect due to the spike (S) transmembrane glycoprotein. IBV has a remarkable capacity for genetic recombination and mutation, resulting in many genotypes and antigenic variants over evolutionary time. Currently, it is classified into nine genetic types (GI to GIX) and 41 (1 to 41) lineages disseminated worldwide. In South America, IBV was first identified in early commercial poultry production ventures in Brazil in the 1950s. Since then, this virus has been frequently detected in commercial South American poultry farms, being classified into serotypes in the first decades and genotypes more recently. IBVs of the Massachusetts (Mass) serotype were initially detected and vaccine strains of this serotype were used extensively on commercial poultry farms. Other serotypes/genotypes were identified later, with almost all of them classified in the current genetic type I (GI). In addition, five GI lineages (GI-1, -11, -13, -16, and -23) have been associated with the main infectious bronchitis outbreaks in the continent, with some variations in the occurrence according to the countries and the period of time. Molecular epidemiological surveillance of IBV genetic types and lineages is necessary to anticipate potential outbreaks, revealing patterns of viral evolution and dissemination, as well as to guide the selection of appropriate vaccine strains and immunization programs. Full article

Infectious bronchitis virus (IBV) of the GI-23 lineage, which first emerged in the Middle East in the late 1990s, has since spread worldwide. The factors driving its expansion, whether human involvement, wild bird migration, or the virus’s biological traits, are still unclear. This study aimed to trace the genome evolution of GI-23 IBV in chickens and its adaptability to quails, which are susceptible to both gamma- and deltacoronaviruses. Thirty specific-pathogen-free (SPF) birds, aged between two and three weeks, were used. Initially, three birds were inoculated with the G052/2016 IBV via the oculo-nasal route. On the third day post-infection (dpi), oropharyngeal swabs were collected from the whole group, pooled, and subsequently used to infect three next birds. This process was repeated nine more times during consecutive IBV passages (P-I–P-X), and eventually, virus sequencing was performed using Next-Generation Sequencing (NGS). The obtained results showed that quails were not susceptible to the IBV GI-23 lineage, as the virus RNA was detected in low amounts only during the first passage (QP-I) with no further detections in later rounds of IBV passaging. In chickens, only mild diarrhea symptoms appeared in a few individuals. The NGS analysis identified sixty-two single nucleotide variants (SNVs), thirty of which caused amino acid changes, twenty-eight were synonymous, and one SNV introduced a stop codon. Three SNVs were found in untranslated regions. However, none of these SNVs lasted beyond seven passages, with forty-four being unique SNVs. The Shannon entropy values measured during passages varied for pol1a, pol1b, S, 5a, 5b, and N genes, with overall genome complexity peaking at CP-VI and CP-X. The highest complexity was observed in the pol1a (CP-X) and S genes (CP-IV, CP-VI, CP-VIII, and CP-X). Along with the S gene that was under positive selection, eight codons in pol1a were also positively selected. These findings suggest that even in an adapted host, IBV variability does not stabilize without immune pressure, indicating continuous molecular changes within its genome. Full article

This contribution is aimed at analyzing a series of life-prolonging and rejuvenating treatments (bcud len), recipes of ambrosia for immortality (bdud rtsi sman), and yogic and meditative techniques incorporated in the Man ngag bye ba ring bsrel (Ten Million of Quintessential Instructions, The Relics; henceforth Ring bsrel), a medical corpus mainly authored by Zur mkhar ba mNyam nyid rdo rje (1439–1475). The many treads of mNyam nyid rdo rje’s literary production reflect his rNying ma and bKa’ brgyud spiritual legacies: the author systematically elaborated materials drawn from the rNying ma gter ma tradition and complex medico–alchemical practices ascribed to the third Karmapa Rang byung rdo rje (1284–1339) and O rgyan pa rin chen dpal (1230–1309). The key ingredients of the recipes include saxifrage [bdud rtsi ’od ldan; Micranthes melanocentra; Saxifraga melanocentra], purple sage [lug mur; Phlomoides bracteosa], potent substances such as black aconite [bstan dug; Aconitum spicatum;], nightshade [thang phrom; Anisodus spp.; Mandragora caulescens], mercury–sulfide ashes (zla bcud; bcud rgyal), aphrodisiacs containing salamander meat [da byid, gangs sbal; Batrachuporus pinchonii], caterpillar fungus [dByar rtswa dgun ’bu; Cordyceps sinensis], and other substances endowed with hot potencies that can enhance gtum mo practices such as the dwarf rhododendron [da lis; Rhododendron spp.] and compounds containing long peer [pi pi ling; Piper longum], black pepper, [pho bar is; Piper nigrum], ginger, and so forth. The consecrated medicines and the rituals can bestow protection from any sort of diseases, diseases-carrier forces (gdon), and poisoning and lead to spiritual achievements. The analysis of these scriptural materials brings into focus the historical interrelation of diverse traditions that are represented by the heterogeneity of ideas and practices handed down through the Zur medical lineage. Full article

Infectious bronchitis virus (IBV) poses a significant threat to poultry worldwide, necessitating robust surveillance and vaccination strategies. This study aimed to conduct IBV surveillance in Brazil, assess potential vaccine viral escapes, and evaluate vaccine persistence in vaccinated broilers. A total of 1000 tracheal swabs from 100 flocks across six states were analyzed using RT-PCR. The results showed that 91% of the flocks tested positive for IBV. The detected strains included GI-1, GI-11, and GI-23. Notably, 90% of batches received vaccines containing either GI-1 or GI-11 lineages. The study revealed vaccine persistence in 67 samples between days 16 and 32 post-vaccination. In contrast, unvaccinated batches had a high prevalence of IBV GI-11 strains (70%). These findings highlight widespread IBV circulation in Brazil with persistent viral presence in vaccinated birds and wild viruses in unvaccinated ones. Collectively, the data reveal a widespread presence of IBV in Brazil, characterized by prolonged viral persistence in vaccinated animals and the occurrence of wild viruses in both unvaccinated birds and those vaccinated against specific strains. It can be concluded from this study that there was a widespread occurrence of IBV in Brazil, providing long viral persistence in vaccinated animals, as well as the occurrence of wild virus in unvaccinated birds or birds vaccinated against individual strains. Full article

Magnoliaceae, an ancient lineage of relict plants, were once extensively distributed throughout geological history. Understanding their species diversity, geographic distribution patterns, and hotspots is essential for providing a theoretical foundation for germplasm resource assessment, conservation, and utilization. This study presents a comprehensive catalog of wild Magnoliaceae species in China, derived from an extensive literature review integrating geographic distribution and endemism data. Utilizing GIS 10.2 software, we analyzed data from up to July 2024, revealing that China hosts 157 wild Magnoliaceae species across 13 genera, including 11 varieties, two subspecies, and three forms. These species are distributed across 24 provincial-level administrative regions, including special administrative regions and municipalities. Yunnan Province exhibits the highest species richness, with 12 genera and 94 species, followed by Guizhou, with 9 genera and 65 species, and Guangxi, with 9 genera and 62 species. At the county level, species are found in 609 regions, with Malipo County in Yunnan recording the highest count (32 species), followed by Leishan County in Guizhou (28 species). Vertically, Magnoliaceae are most abundant in the H3 elevation band (1000 < H3 ≤ 1500 m), while the H7 elevation band (H7 > 3000 m) shows the lowest species diversity. China has two endemic genera, Pachylarnax and Woonyoungia, along with 102 endemic species, of which Michelia accounts for the highest number of endemics at 33. The species composition in Guizhou shows significant similarity to that in Guangxi, Sichuan, and Yunnan, indicating close phylogenetic relationships among these floras. The Yunnan–Guizhou–Guangxi region is identified as a “modern distribution center”, “diversity preservation center”, “hotspot”, and “refuge” for wild Magnoliaceae in China. This study highlights the importance of understanding the diversity and distribution patterns of wild Magnoliaceae for the effective conservation, development, and sustainable utilization of plant resources. Full article