Search Results (2,238)

SARS-CoV-2 undergoes frequent mutations that drive viral evolution and genomic diversity, influencing transmissibility, immune escape, and disease severity. In this study, we performed whole-genome sequencing on SARS-CoV-2 isolates from patients in New York City and identified several globally rare mutations across multiple viral lineages. The isolates analyzed for rare mutations belonged to three lineages: B.1.1.7 (Alpha), B.1.526 (Iota), and B.1.623. We identified 16 rare mutations (global incidence <1000) in non-structural protein genes, including nsp2, nsp3, nsp4, nsp6, nsp8, nsp13, nsp14, ORF7a, and ORF8. Three of these mutations—located in nsp2, nsp13, and ORF8—have been reported in fewer than 100 individuals worldwide. We also detected five rare mutations in structural proteins (S, M, and N), including two—one in M and one in N—previously reported in fewer than 100 cases globally. We present clinical profiles of three patients, each infected with genetically distinct viral isolates from the three lineages studied. Furthermore, we illustrate a local transmission chain inferred from unique mutation patterns identified in the Omicron genome. These findings underscore the importance of whole-genome sequencing for detecting rare mutations, tracking community spread, and identifying emerging variants with clinical and public health significance. Full article

Monkeypox virus (MPXV) has caused 148,892 confirmed cases and 341 deaths from 137 countries worldwide, as reported by the World Health Organization (WHO), highlighting the urgent need for effective vaccines to prevent the spread of MPXV. Traditional vaccine development is low-throughput, expensive, time consuming, and susceptible to reversion to virulence. Alternatively, a reverse vaccinology approach offers a rapid, efficient, and safer alternative for MPXV vaccine design. Here, MPXV proteins associated with viral infection were analyzed for immunogenic epitopes to design multi-epitope vaccines based on B-cell, CD4+, and CD8+ epitopes. Epitopes were selected based on allergenicity, antigenicity, and toxicity parameters. The prioritized epitopes were then combined via peptide linkers and N-terminally fused to various protein adjuvants, including PADRE, beta-defensin 3, 50S ribosomal protein L7/12, RS-09, and the cholera toxin B subunit (CTB). All vaccine constructs were computationally validated for physicochemical properties, antigenicity, allergenicity, safety, solubility, and structural stability. The three-dimensional structure of the selected construct was also predicted. Moreover, molecular docking and molecular dynamics (MD) simulations between the vaccine and the TLR-4 immune receptor demonstrated a strong and stable interaction. The vaccine construct was codon-optimized for high expression in the E. coli and was finally cloned in silico into the pET21a (+) vector. Collectively, these results could represent innovative tools for vaccine formulation against MPXV and be transformative for other infectious diseases. Full article

Foodborne diseases are the most common causes of illness worldwide. Bacterial pathogens, including Staphylococcus aureus, are often involved in foodborne disease and pose a serious threat to human health. S. aureus is commonly found in humans and a variety of animal species. Staphylococcal enteric disease, specifically staphylococcal food poisoning (SFP), accounts for numerous gastrointestinal illnesses, through the contamination of food with its enterotoxins, and its major impact on human health imposes a heavy economic burden in society. Commonly, antibiotics and antimicrobials are used to treat SFP. However, a range of complications may arise with these treatments, impeding the control of S. aureus diseases specifically caused by methicillin-resistant S. aureus (MRSA). Natural alternative options to control S. aureus diseases, such as bacteriophages, plant-based antimicrobials, nanoparticle-based or light-based therapeutics, and probiotics, are promising in terms of overcoming these existing problems as they are environmentally friendly, abundant, unlikely to induce resistance in pathogens, cost-effective, and safe for human health. Recent findings have indicated that these alternatives may reduce the colonization and infection of major foodborne pathogens, including MRSA, which is crucial to overcome the spread of antibiotic resistance in S. aureus. This review focuses on the present scenario of S. aureus in foodborne disease, its economic importance and current interventions and, most importantly, the implications of natural antimicrobials, especially probiotics and synbiotics, as alternative antimicrobial means to combat pathogenic microorganisms particularly, S. aureus and MRSA. Full article

The intensifying global competition for cobalt resources and the increasing likelihood of trade decoupling and disruption are profoundly impacting the global energy transition. In a globalized trade environment, a decline in cobalt supply from exporting countries can spread through the trade network, negatively affecting demand countries. Quantitative analysis of the negative impacts of export supply declines in various countries can help identify early risks in the global supply chain, providing a scientific basis for energy security, industrial development, and policy responses. This study constructs a trade network using trade data on metal cobalt, cobalt powder, cobalt concentrate, and ore sand from the upstream (mining, selection, and smelting) stages of the cobalt industry chain across 155 countries and regions from 2000 to 2023. Based on this, an impact diffusion model is established, incorporating the trade volumes and production levels of cobalt resources in each country to measure their resilience to shocks and determine their direct or indirect dependencies. The study then simulates the impact on countries (regions) when each country’s supply is completely interrupted or reduced by 50%. The results show that: (1) The global cobalt trade network exhibits a ‘one superpower, multiple strong players’ characteristic. Congo (DRC) has a far greater destructive power than other countries, while South Africa, Zambia, Australia, Russia, and other countries have higher destructive power due to their strong storage and production capabilities, strong smelting capabilities, or as important trade transit countries. (2) The global cobalt trade network primarily consists of three major risk areas. The African continent, the Philippines and Indonesia in Southeast Asia, Australia in Oceania, and Russia, the United States, China, and the United Kingdom in Eurasia and North America form the primary risk zones for global cobalt trade. (3) When there is a complete disruption or a 50% reduction in export supply, China will suffer the greatest average demand loss, far exceeding the second-tier countries such as the United States, South Africa, and Zambia. In contrast, European countries and other regions worldwide will experience the smallest average demand loss. Full article

Hepatitis E virus (HEV) is a pathogen that has caused various epidemics and sporadic localized cases. It is considered to be a public health problem worldwide. HEV is a small RNA virus with a significant genetic diversity, a broad host range, and a heterogeneous geographical distribution. HEV is mainly transmitted via the faecal–oral route. However, some animals are considered to be natural or potential reservoirs of HEV, thus elucidating the zoonotic route of transmission via the environment through contact with these animals or consumption of their by-products. Other routes of human-to-human transmission are not negligible. The various human–animal–environment entities, taken under one health approach, show the circulation and involvement of the different species (mainly Paslahepevirus balayani and Rocahepevirus ratti) and genotypes in the spreading of HEV infection. Regarding P. balayani, eight genotypes have been described, of which five genotypes (HEV-1 to 4 and HEV-7) are known to infect humans, while six have been reported to infect animals (HEV-3 to HEV-8). Furthermore, the C1 genotype of the rat HEV strain (HEV-C1) is known to be more frequently involved in human infections than the HEV-C2 genotype, which is known to infect mainly ferrets and minks. Contamination can occur during run-off, flooding, and poor sanitation, resulting in all of these genotypes being disseminated in the environment, contaminating both humans and animals. This systematic review followed the PRISMA guidelines and was registered in PROSPERO 2025 CRD420251071192. This research highlights the importance of investigating the transmission routes and major circulating HEV genotypes in order to adopt a holistic approach for controlling its emergence and preventing future outbreaks. In addition, this article outlines the knowledge of HEV in Africa, underlining the absence of large-scale studies at the environmental, human, and animal levels, which could improve HEV surveillance on the continent. Full article

Arundo donax L. has been introduced in markets worldwide due to its economic value. However, it is listed in the world’s 100 worst alien invasive species because it easily escapes from cultivation, and forms dense monospecific stands in riparian areas, agricultural areas, and grassland areas along roadsides, including in protected areas. This species grows rapidly and produces large amounts of biomass due to its high photosynthetic ability. It spreads asexually through ramets, in addition to stem and rhizome fragments. Wildfires, flooding, and human activity promote its distribution and domination. It can adapt to various habitats and tolerate various adverse environmental conditions, such as cold temperatures, drought, flooding, and high salinity. A. donax exhibits defense mechanisms against biotic stressors, including herbivores and pathogens. It produces indole alkaloids, such as bufotenidine and gramine, as well as other alkaloids that are toxic to herbivorous mammals, insects, parasitic nematodes, and pathogenic fungi and oomycetes. A. donax accumulates high concentrations of phytoliths, which also protect against pathogen infection and herbivory. Only a few herbivores and pathogens have been reported to significantly damage A. donax growth and populations. Additionally, A. donax exhibits allelopathic activity against competing plant species, though the allelochemicals involved have yet to be identified. These characteristics may contribute to its infestation, survival, and population expansion in new habitats as an invasive plant species. Dense monospecific stands of A. donax alter ecosystem structures and functions. These stands impact abiotic processes in ecosystems by reducing water availability, and increasing the risk of erosion, flooding, and intense fires. The stands also negatively affect biotic processes by reducing plant diversity and richness, as well as the fitness of habitats for invertebrates and vertebrates. Eradicating A. donax from a habitat requires an ongoing, long-term integrated management approach based on an understanding of its invasive mechanisms. Human activity has also contributed to the spread of A. donax populations. There is an urgent need to address its invasive traits. This is the first review focusing on the invasive mechanisms of this plant in terms of adaptation to abiotic and biotic stressors, particularly physiological adaptation. Full article

The spotted wing drosophila, Drosophila suzukii is an injurious polyphagous pest threatening worldwide soft fruit production. Its high adaptability to new colonized environments, short life cycle, and wide host range are supporting its rapid spread. The most common techniques to reduce its significant economic damage are based on multiple insecticides applications per season, even prior to the harvest, which reduces agroecosystem biodiversity and affects human and animal health. Environmental concerns and regulatory restrictions on insecticide use are driving the need for studies on alternative biological control strategies. This study aimed to assess the effect of T. drosphilae in controlling D. suzukii infestations and its interaction with P. vindemiae, a secondary parasitoid naturally present in Apulia (South Italy). Field experiments were carried out in organic cherry orchards in Gioia del Colle (Bari, Italy) to test the efficacy and adaptability of T. drosphilae following weekly releases of artificially reared individuals. Additionally, the interaction between P. vindemiae and T. drosphilae was studied under laboratory conditions. Results from field experiments showed that D. suzukii populations were significantly lower when both parasitoids were present. However, T. drosophilae was less prone to adaptation, so its presence and parasitism were limited to the post-release period. Laboratory experiments, instead, confirmed the high reduction of D. suzukii populations when both parasitoids are present. However, the co-existence of the two parasitoids resulted in a reduced parasitism rate and offspring production, notably for T. drosophilae. This competitive disadvantage may explain its poor establishment in field conditions. These findings suggest that the field release of the two natural enemies should be carried out with reference to their natural population abundance to not generate competition effects. Full article

One of the most challenging problems in data analysis is visualizing patterns and extracting insights from multi-dimensional datasets that vary over time. The complexity of data and variations in the correlations between different features adds further difficulty to the analysis. In this paper, we provide a framework to analyze the temporal dynamics of such datasets. We use machine learning clustering techniques and examine the time evolution of data patterns by constructing the corresponding cluster trajectories. These trajectories allow us to visualize the patterns and the changing nature of correlations over time. The similarity and correlations of features are reflected in common cluster membership, whereas the historical dynamics are described by a trajectory in the corresponding (cluster, time) space. This allows an effective visualization of multi-dimensional data over time. We introduce several statistical metrics to measure duration, volatility, and inertia of changes in patterns. Using the Hamming distance of trajectories over multiple time periods, we propose a novel metric, the Hamming diversification index, to measure the spread between trajectories. The novel metric is easy to compute, has a simple machine learning implementation, and provides additional insights into the temporal dynamics of data. This parsimonious diversification index can be used to examine changes in pattern similarities over aggregated time periods. We demonstrate the efficacy of our approach by analyzing a complex multi-year dataset of multiple worldwide economic indicators. Full article

Microbial infections are an escalating global health threat, driven by the alarming rise of antimicrobial resistance (AMR), which has made many conventional antibiotics increasingly ineffective and threatens to reverse decades of medical progress. The rapid emergence and spread of multidrug-resistant bacteria have severely limited treatment options, resulting in increased morbidity, mortality, and healthcare burden worldwide. In response to these challenges, phage therapy is regaining interest as a promising alternative. Bacteriophages, the most abundant biological entities, have remarkable specificity toward their bacterial hosts, enabling them to selectively eliminate pathogenic strains. Phage therapy presents several advantages over conventional antibiotics, which include minimal disruption to the microbiome and a slower rate of resistance development. Among the various sources of phages, the marine environment remains one of the least explored. Given their adaptation to saline conditions, high pressure, and variable nutrient levels, marine bacteriophages mostly exhibit enhanced environmental stability, broader host ranges, and distinct infection mechanisms, thus making them highly promising for therapeutic purposes. This review explores the growing therapeutic potential of marine bacteriophages by examining their ecological diversity, biological characteristics, infection dynamics, and practical applications in microbial disease control. It also deals with emerging strategies such as phage–antibiotic synergy, genetic engineering, and the use of phage-derived enzymes, alongside several challenges that must be addressed to enable clinical translation and regulatory approval. Advancing our understanding and application of marine phages presents a promising path in the global fight against AMR and the development of next-generation antimicrobial therapies. Full article

Recent studies have detected microplastics (MPs) in seafood and various food products worldwide, including poultry, fish, salt, beverages, fruits, and vegetables. This widespread contamination makes human exposure through consumption unavoidable and raises concerns for food safety and human health. MPs provide physical support to microorganisms for biofilm formation, protecting them from extreme conditions and facilitating their persistence in the environment. However, little is known about the impact of MPs in the transmission of foodborne pathogens and subsequent spread of infectious diseases like campylobacteriosis, the most common foodborne illness caused by a bacterium, Campylobacter. This review explores the sources of MP contamination in the food chain and offers a comprehensive overview of MP presence in animals, food products, and beverages. Moreover, we compile the available studies linking MPs and Campylobacter and examine the potential impact of these particles on the transmission of Campylobacter along the food chain with a particular focus on poultry, the main source and reservoir for the pathogen. While the environmental and toxicological effects of MPs are increasingly understood, their influence on the virulence of Campylobacter and the spread of antimicrobial resistance remains underexplored. Further studies are needed to develop standardized methods for isolating and identifying MPs, enabling comprehensive investigations and more effective monitoring and risk mitigation strategies. Full article

Ailanthus altissima (AA) is an invasive tree species rapidly spreading worldwide, colonizing both urban and agricultural or forestry environments. This three-year study aimed to assess its effects on the growth and yield traits of the Koroneiki olive cultivar under co-cultivation in pots, combined with two irrigation regimes, full and deficit irrigation (60% of full). Within each irrigation regime, olive trees were grown either in the presence or absence (control) of AA. The trial evaluated several parameters, including vegetative growth, yield traits, and oil quality characteristics. Co-cultivation with AA had no significant impact on tree growth after three years, though it significantly reduced oil content per fruit. Antioxidant capacity of the oil improved under deficit irrigation, while AA presence did not significantly affect it, except for an increase in o-diphenol concentration. Neither the fatty acid profile nor squalene levels were significantly influenced by either treatment. Fruit weight and color were primarily affected by deficit irrigation. During storage, olive oil quality declined significantly, with pre-harvest treatments (presence or absence of AA and full or deficit irrigation regime) playing a critical role in modulating several quality parameters. In conclusion, the presence of AA near olive trees did not substantially affect the key quality indices of the olive oil, which remained within the criteria for classification as extra virgin. Full article

The intersection of microbial food safety and antimicrobial resistance (AMR) represents a mounting global threat with profound implications for public health, food safety, and sustainable development. This review explores the complex pathways through which foodborne pathogens—such as Salmonella spp., Escherichia coli (E. coli), Listeria monocytogenes (L. monocytogenes), and Campylobacter spp.—acquire and disseminate resistance within human, animal, and environmental ecosystems. Emphasizing a One Health framework, we examine the drivers of AMR across sectors, including the misuse of antibiotics in agriculture, aquaculture, and clinical settings, and assess the role of environmental reservoirs in sustaining and amplifying resistance genes. We further discuss the evolution of surveillance systems, regulatory policies, and antimicrobial stewardship programs (ASPs) designed to mitigate resistance across the food chain. Innovations in next-generation sequencing, metagenomics, and targeted therapeutics such as bacteriophage therapy, antimicrobial peptides (AMPs), and CRISPR-based interventions offer promising alternatives to conventional antibiotics. However, the translation of these advances into practice remains uneven, particularly in low- and middle-income countries (LMICs) facing significant barriers to diagnostic access, laboratory capacity, and equitable treatment availability. Our analysis underscores the urgent need for integrated, cross-sectoral action—anchored in science, policy, and education—to curb the global spread of AMR. Strengthening surveillance, investing in research, promoting responsible antimicrobial use, and fostering global collaboration are essential to preserving the efficacy of existing treatments and ensuring the microbiological safety of food systems worldwide. Full article

Orthoflaviviruses (formerly flaviviruses) are known for their role in numerous diseases affecting both humans and animals. Despite the worldwide distribution of orthoflaviviruses, individual species are only found in endemic or epidemic regions. However, in recent decades, certain orthoflaviviruses have spread beyond their traditional geographic boundaries, even crossing continents. Given the long-distance movements of birds, the knowledge of zoonotic orthoflaviviruses associated with birds is essential because of their possible introduction into new regions, as was the case with West Nile virus and Usutu virus. A thorough literature review was conducted on zoonotic orthoflaviviruses related to birds, including lesser-known (re-)emerging and neglected orthoflaviviruses that are limited to specific regions and/or avian hosts but have the potential to spread to a wider geographical area and pose a higher risk of transmission to humans. Several of these viruses possess significant zoonotic potential and can cause a wide spectrum of diseases in humans, ranging from mild febrile illnesses (Zika virus) to severe neuroinvasive diseases (tick-borne encephalitis, West Nile, Japanese encephalitis virus) and hemorrhagic fevers (yellow fever, dengue virus). Geographic distribution, hosts, vectors, incidence of human infections, and impact on human and animal health of zoonotic flaviviruses related to birds are critically reviewed. The viruses have been categorized based on the role of birds as an orthoflavivirus host and the clinical presentation in human infections. Full article

Banana is an important cash and food crop worldwide. Recent outbreaks of banana diseases are threatening the global banana industry and smallholder livelihoods. Remote sensing data offer the potential to detect the presence of disease, but formal analysis is needed to compare inferred disease data with observed disease data. In this study, we present a novel remote-sensing-based framework that combines Landsat-8 imagery with meteorology-informed phenological models and machine learning to identify anomalies in banana crop health. Unlike prior studies, our approach integrates domain-specific crop phenology to enhance the specificity of anomaly detection. We used a pixel-level random forest (RF) model to predict 11 key vegetation indices (VIs) as a function of historical meteorological conditions, specifically daytime and nighttime temperature from MODIS and precipitation from NASA GES DISC. By training on periods of healthy crop growth, the RF model establishes expected VI values under disease-free conditions. Disease presence is then detected by quantifying the deviations between observed VIs from Landsat-8 imagery and these predicted healthy VI values. The model demonstrated robust predictive reliability in accounting for seasonal variations, with forecasting errors for all VIs remaining within 10% when applied to a disease-free control plantation. Applied to two documented outbreak cases, the results show strong spatial alignment between flagged anomalies and historical reports of banana bunchy top disease (BBTD) and Fusarium wilt Tropical Race 4 (TR4). Specifically, for BBTD in Australia, a strong correlation of 0.73 was observed between infection counts and the discrepancy between predicted and observed NDVI values at the pixel with the highest number of infections. Notably, VI declines preceded reported infection rises by approximately two months. For TR4 in Mozambique, the approach successfully tracked disease progression, revealing clear spatial spread patterns and correlations as high as 0.98 between VI anomalies and disease cases in some pixels. These findings support the potential of our method as a scalable early warning system for banana disease detection. Full article

The whitefly, Bemisia tabaci, is a complex of cryptic species that is a significant pest of different legume hosts that inhabits various regions worldwide with diverse climates and characteristics. Its adaptability is often facilitated by the insect’s microbiome, which can contribute to both the metabolism of host plant secondary compounds and insecticide resistance. The most relevant biotypes in Brazil are Middle East-Asia Minor 1 (MEAM1) and Mediterranean (MED), because of their ability to damage different hosts. Although MEAM1 is the prevalent species in Brazil, MED has great potential to spread, and there is little current knowledge about the biology of this biotype in the country. Therefore, the objective of this study was to evaluate the development and viability of MED on two legumes, soybean and common bean, alongside cotton, bell pepper, and tomato, at temperatures of 20 °C, 23 °C, 26 °C, 29 °C, 32 °C, and 35 °C and characterize the composition of its endosymbionts. Temperatures between 23 °C and 32 °C were the most suitable for B. tabaci MED development and viability across all tested host plants, whereas 35 °C proved harmful for insects reared on legumes. We observed a temperature threshold (°C) and thermal constant (degree-days) that varied according to the host plant, ranging from 9.81 °C and 384.62 for soybean to 11.17 °C and 333.33 for bell pepper, respectively. The main endosymbionts were in a ratio of 80% Hamiltonella and 20% Cardinium. These results allow the future mapping of risk for the MED biotype on different host plants in Brazil and elsewhere in South America. Full article