Search Results (49)

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

Infectious Bronchitis Virus (IBV) is a major threat to the poultry industry worldwide, causing significant economic losses. While the virus’s genetic structure is well understood, the specific strains circulating in Bolivia have remained uncharacterized until now. This study aimed to identify and characterize new IBV strains in Bolivia. Tissue samples from broilers exhibiting clinical signs of Infectious Bronchitis were screened to detect IBV using real-time RT-PCR (RT-qPCR). Positive samples with low cycle threshold (Ct) values were selected for sequencing the full S1 gene. Of the 12 samples analyzed, 10 were determined to be positive for IBV. However, only four samples yielded sufficient genetic material for sequencing and subsequent phylogenetic analysis. The results revealed the presence of GI-1 and GI-23 lineages, both belonging to genotype I (GI). The GI-1 lineage showed >99% sequence identity to the H120 and Massachusetts vaccine strains, suggesting a close relationship. In contrast, the GI-23 lineage clustered with other IBV strains, showing a distinct subclade that is genetically distant from Brazilian strains. No evidence of recombination was found. Furthermore, amino acid substitution analysis identified specific mutations in the S1 subunit, particularly in the hypervariable regions 1, 2, and 3. These mutations could potentially alter the virus’s antigenicity, leading to reduced vaccine efficacy. The findings of this study highlight the importance of continued and broad genomic surveillance of circulating IBV strains and the need to improve vaccination strategies in Bolivia. Full article

Understanding the spatial morphological characteristics and driving factors of rural settlements in ethnic minority areas is crucial for the conservation and tourism development of ethnic villages. Accordingly, this study employs Shuanglang Town, China as a case study, adopting an integrated approach that combines spatial syntax analysis, the optimal parameter geodetector model, and GIS spatial analysis techniques. This comprehensive methodology systematically investigates the spatial morphological features, differentiation characteristics, and influencing factors of ethnic villages. The findings reveal the logical lineage and formation mechanisms underlying the overall layout, street network, and public spaces of the villages. Specifically, the results demonstrate (1) a discernible gradation in spatial configurations, transitioning from compact “back mountain villages” in the northeast to more dispersed “seaside villages” in the southwest, with notable disparities in accessibility among different villages; (2) topography, water distribution, and water quality as the dominant factors shaping village spatial patterns; (3) the interactive and heterogeneous effects of multiple natural and anthropogenic factors, including topography, water resources, agricultural practices, and ethnic cultural traditions, significantly influencing the spatial morphology of villages; and (4) common principles governing the site selection of different ethnic village typologies, reflecting the villagers’ understanding and intelligent utilization of the natural environment. This study contributes to comprehending the spatial characteristics of rural settlements in ethnic minority areas and provides a theoretical and practical foundation for advancing analogous rural revitalization initiatives. The findings offer insights into the spatial logic and formation processes of ethnic villages, informing conservation efforts and sustainable tourism development strategies. Full article

Regional ecological protection is an urgent task in today’s social development, and constructing an ecological protection network is an important way to achieve regional ecological coordination. However, previous studies have lacked a systematic review and analysis of policy document transmission paths, failing to consider the spatial network structure and its complex characteristics of regional ecological protection policies, resulting in deficiencies in regional coordinated governance of the ecological environment. To address this gap, this study constructs an ecological policy transmission network lineage for the Chengdu Plain urban agglomeration (CDPUA) based on 400 ecological environmental protection policy documents issued by cities in the CDPUA from 2015 to 2022, focusing on the transmission perspective of policy documents. Social network analysis methods, a GIS spatial analysis, and other methods were employed to construct the ecological protection network of the CDPUA and analyze the complex spatial structure and characteristics of the network. It was found that the integrated ecological protection network of the CDPUA exhibits a multi-core triangular pattern with spatial characteristics of density in the east and sparsity in the west. The integrated ecological protection network has a density of 60.71%, indicating a strong intercity linkage, with Suining as the central nucleus transmitting policies to surrounding cities, forming the Suining–Chengdu–Mianyang policy transmission triangle. The urban agglomeration has formed an ecological protection network dominated by multiple cities, offering diverse and distinct types of ecosystem services. This study provides insights to enhance regional collaborative ecological governance and protection, promoting sustainable development in the region. Full article

The QXL87 live attenuated vaccine strain for infectious bronchitis represents the first approved QX type (GI-19 lineage) vaccine in China. This strain was derived from the parental strain CK/CH/JS/2010/12 through continuous passage in SPF chicken embryos. To elucidate the molecular mechanism behind its attenuation, whole-genome sequencing was conducted on both the parental and attenuated strains. Analysis revealed 145 nucleotide mutations in the attenuated strain, leading to 48 amino acid mutations in various proteins, including Nsp2 (26), Nsp3 (14), Nsp4 (1), S (4), 3a (1), E (1), and N (1). Additionally, a frameshift mutation caused by a single base insertion in the ORFX resulted in a six-amino-acid extension. Subsequent comparison of post-translational modification sites, protein structure, and protein–protein binding sites between the parental and attenuated strains identified three potential virulence genes: Nsp2, Nsp3, and S. The amino acid mutations in these proteins not only altered their conformation but also affected the distribution of post-translational modification sites and protein–protein interaction sites. Furthermore, three potential functional mutation sites—P106S, A352T, and L472F, all located in the Nsp2 protein—were identified through PROVEAN, PolyPhen, and I-Mutant. Overall, our findings suggest that Nsp2, Nsp3, and S proteins may play a role in modulating IBV pathogenicity, with a particular focus on the significance of the Nsp2 protein. This study contributes to our understanding of the molecular mechanisms underlying IBV attenuation and holds promise for the development of safer live attenuated IBV vaccines using reverse genetic approaches. Full article

Gammacoronavirus infectious bronchitis virus (IBV) causes a highly contagious disease in chickens and seriously endangers the poultry industry. The emergence and co-circulation of diverse IBV serotypes and genotypes with distinct pathogenicity worldwide pose a serious challenge to the development of effective intervention measures. In this study, we report the epidemic trends of IBV in China from 2019 to 2023 and a comparative analysis on the antigenic characteristics and pathogenicity of isolates among major prevalent lineages. Phylogenetic and recombination analyses based on the nucleotide sequences of the spike (S) 1 gene clustered a total of 205 isolates into twelve distinct lineages, with GI-19 as a predominant lineage (61.77 ± 4.56%) exhibiting an overall increasing trend over the past five years, and demonstrated that a majority of the variants were derived from gene recombination events. Further characterization of the growth and pathogenic properties of six representative isolates from different lineages classified four out of the six isolates as nephropathogenic types with mortality rates in one-day-old SPF chickens varying from 20–60%, one as a respiratory type with weak virulence, and one as a naturally occurring avirulent strain. Taken together, our findings illuminate the epidemic trends, prevalence, recombination, and pathogenicity of current IBV strains in China, providing key information for further strengthening the surveillance and pathogenicity studies of IBV. Full article

Infectious bronchitis virus (IBV) causes a highly contagious respiratory disease in chickens, leading to significant economic losses in the poultry industry worldwide. IBV exhibits a high mutation rate, resulting in the continuous emergence of new variants and strains. A complete genome analysis of IBV is crucial for understanding its characteristics. However, it is challenging to obtain whole-genome sequences from IBV-infected clinical samples due to the low abundance of IBV relative to the host genome. Here, we present a novel approach employing next-generation sequencing (NGS) to directly sequence the complete genome of IBV. Through in silico analysis, six primer pairs were designed to match various genotypes, including the GI-19 lineage of IBV. The primer sets successfully amplified six overlapping fragments by long-range PCR and the size of the amplicons ranged from 3.7 to 6.4 kb, resulting in full coverage of the IBV genome. Furthermore, utilizing Illumina sequencing, we obtained the complete genome sequences of two strains belonging to the GI-19 lineage (QX genotype) from clinical samples, with 100% coverage rates, over 1000 × mean depth coverage, and a high percentage of mapped reads to the reference genomes (96.63% and 97.66%). The reported method significantly improves the whole-genome sequencing of IBVs from clinical samples; thus, it can improve understanding of the epidemiology and evolution of IBVs. Full article

The GI-19 lineage of infectious bronchitis virus (IBV) has emerged as one of the most impactful, particularly in the “Old World”. Originating in China several decades ago, it has consistently spread and evolved, often forming independent clades in various areas and countries, each with distinct production systems and control strategies. This study leverages this scenario to explore how different environments may influence virus evolution. Through the analysis of the complete S1 sequence, four datasets were identified, comprising strains of monophyletic clades circulating in different continents or countries (e.g., Asia vs. Europe and China vs. Thailand), indicative of single introduction events and independent evolution. The population dynamics and evolutionary rate variation over time, as well as the presence and intensity of selective pressures, were estimated and compared across these datasets. Since the lineage origin (approximately in the mid-20th century), a more persistent and stable viral population was estimated in Asia and China, while in Europe and Thailand, a sharp increase following the introduction (i.e., 2005 and 2007, respectively) of GI-19 was observed, succeeded by a rapid decline. Although a greater number of sites on the S1 subunit were under diversifying selection in the Asian and Chinese datasets, more focused and stronger pressures were evident in both the European (positions 2, 52, 54, 222, and 379 and Thai (i.e., positions 10, 12, 32, 56, 62, 64, 65, 78, 95, 96, 119, 128, 140, 182, 292, 304, 320, and 323) strains, likely reflecting a more intense and uniform application of vaccines in these regions. This evidence, along with the analysis of control strategies implemented in different areas, suggests a strong link between effective, systematic vaccine implementation and infection control. However, while the overall evolutionary rate was estimated at approximately 10⁻³ to 10⁻⁴, a significant inverse correlation was found between viral population size and the rate of viral evolution over time. Therefore, despite the stronger selective pressure imposed by vaccination, effectively constraining the former through adequate control strategies can efficiently prevent viral evolution and the emergence of vaccine-escaping variants. Full article

Sapovirus (SaV) is a type of gastroenteric virus that can cause acute gastroenteritis. It is highly contagious, particularly among children under the age of 5. In this study, a total of 712 stool samples from children under the age of 5 with acute gastroenteritis were collected. Out of these samples, 28 tested positive for SaV, resulting in a detection rate of 3.93% (28/712). Samples with Ct < 30 were collected for library construction and high-throughput sequencing, resulting in the acquisition of nine complete genomes. According to Blast, eight of them were identified as GI.1, while the remaining one was GI.6. The GI.6 strain sequence reported in our study represents the first submission of the GI.6 strain complete genome sequence from mainland China to the Genbank database, thus filling the data gap in our country. Sequence identity analysis revealed significant nucleotide variations between the two genotypes of SaV and their corresponding prototype strains. Phylogenetic and genetic evolution analyses showed no evidence of recombination events in the obtained sequences. Population dynamics analysis demonstrated potential competitive inhibition between two lineages of GI.1. Our study provides insights into the molecular epidemiological and genetic evolution characteristics of SaV prevalent in the Nantong region of China, laying the foundation for disease prevention and control, as well as pathogen tracing related to SaV in this area. Full article

Southeastern Zhejiang boasts a large number of ancient architectural heritage sites and features, representing a rich cultural heritage. However, this region lacks a unified and effective planning system and coordination mechanism. Each county and city operates independently, resulting in low levels of resource sharing and utilization. There is a lack of a long-term, comprehensive, and effective planning and management framework. Therefore, this study focuses on 268 ancient architectural heritage sites in southeastern Zhejiang. By employing correlation analysis methods on the ArcGIS platform, this study summarizes the spatial and temporal distribution characteristics and evolutionary patterns of ancient architectural heritage. The study aims to provide guidance for subsequent comprehensive research, protection, and planning, thereby achieving the sustainable development of the region’s ancient architectural cultural heritage. The conclusions are as follows: (1) Southeastern Zhejiang’s ancient architectural heritage has formed an overall spatial distribution pattern known as the “three cores and three belts”. Targeted sustainable development strategies for ancient architectural heritage can be proposed accordingly. (2) The overall spatial distribution of ancient architectural cultural heritage in southeastern Zhejiang is highly correlated with the natural environment. It is important to consider the correlation between the overall spatial distribution of ancient architectural cultural heritage and the natural environment in the region during subsequent development. (3) The distribution of newly added architectural heritage in southeastern Zhejiang is influenced by factors such as water resource reforms, immigration policies, administrative changes, and cultural ideologies. Throughout history, southeastern Zhejiang has exhibited different spatial distribution structures, laying the foundation for the study of its genealogy and lineage of ancient architectural heritage. The contribution of this research lies in providing targeted references for the coordinated development and systematic revitalization of ancient architectural cultural heritage for the future of southeastern Zhejiang. Full article