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Abstract Background Stool consistency is an important diagnostic criterion in both research and clinical medicine and is often used to define diarrheal disease. Methods We examine the pediatric enteric virome across stool consistencies to evaluate differences in richness and community composition using fecal samples collected from children aged 0 to 5 years participating in a clinical trial in the Amhara region of Ethiopia. The consistency of each sample was graded according to the modified Bristol Stool Form Scale for children (mBSFS-C) before a portion of stool was preserved for viral metagenomic analysis. Stool samples were grouped into 29 pools according to stool consistency type. Differential abundance was determined using negative-binomial modeling. Results Of 446 censused children who were eligible to participate, 317 presented for the study visit examination and 269 provided stool samples. The median age of children with stool samples was 36 months. Species richness was highest in watery-consistency stool and decreased as stool consistency became firmer (Spearman’s r = − 0.45, p = 0.013). The greatest differential abundance comparing loose or watery to formed stool was for norovirus GII (7.64, 95% CI 5.8, 9.5) followed by aichivirus A (5.93, 95% CI 4.0, 7.89) and adeno-associated virus 2 (5.81, 95%CI 3.9, 7.7). Conclusions In conclusion, we documented a difference in pediatric enteric viromes according to mBSFS-C stool consistency category, both in species richness and composition.

BACKGROUND:The enteric viruses shed by different populations can be influenced by multiple factors including access to clean drinking water. We describe here the eukaryotic viral genomes in the feces of Ethiopian children participating in a clean water intervention trial. METHODOLOGY/PRINCIPAL FINDINGS:Fecal samples from 269 children with a mean age of 2.7 years were collected from 14 villages in the Amhara region of Ethiopia, half of which received a new hand-dug water well. Feces from these villages were then analyzed in 29 sample pools using viral metagenomics. A total of 127 different viruses belonging to 3 RNA and 3 DNA viral families were detected. Picornaviridae family sequence reads were the most commonly found, originating from 14 enterovirus and 6 parechovirus genotypes plus multiple members of four other picornavirus genera (cosaviruses, saliviruses, kobuviruses, and hepatoviruses). Picornaviruses with nearly identical capsid VP1 were detected in different pools reflecting recent spread of these viral strains. Next in read frequencies and positive pools were sequences from the Caliciviridae family including noroviruses GI and GII and sapoviruses. DNA viruses from multiple genera of the Parvoviridae family were detected (bocaviruses 1-4, bufavirus 3, and dependoparvoviruses), together with four species of adenoviruses and common anelloviruses shedding. RNA in the order Picornavirales and CRESS-DNA viral genomes, possibly originating from intestinal parasites or dietary sources, were also characterized. No significant difference was observed between the number of mammalian viruses shed from children from villages with and without a new water well. CONCLUSIONS:We describe an approach to estimate the efficacy of potentially virus transmission-reducing interventions and the first complete (DNA and RNA viruses) description of the enteric viromes of East African children. A wide diversity of human enteric viruses was found in both intervention and control groups. Mammalian enteric virome diversity was not reduced in children from villages with a new water well. This population-based sampling also provides a baseline of the enteric viruses present in Northern Ethiopia against which to compare future viromes.

A divergent parvovirus genome was the only eukaryotic viral sequence detected in feces of a Tunisian child with unexplained diarrhea. Tusavirus 1 shared 44% and 39% identity with the nonstructural protein 1 and viral protein 1, respectively, of the closest genome, Kilham rat parvovirus, indicating presence of a new human viral species in the Protoparvovirus genus.

Polyomaviruses are small circular DNA viruses associated with chronic infections and tumors in both human and animal hosts. Using an unbiased deep sequencing approach, we identified a novel, highly divergent polyomavirus, provisionally named MX polyomavirus (MXPyV), in stool samples from children. The ∼5.0 kB viral genome exhibits little overall homology (

The proposed viral genus human Cosavirus (HCoSV) consists of diverse picornaviruses found at high prevalence in the feces of children from developing countries. We sequenced four near-full length genomes and 45 partial VP1 region from HCoSV in human feces from healthy children and children with acute flaccid paralysis in Pakistan, Nigeria and Tunisia and from healthy and diarrhetic adults in Nepal. Genetic analyses of the near-full length genomes revealed presence of a new candidate cosavirus species provisionally labelled as species F (HCoSV-F). A HCoSV genome showed evidence of recombination between species D and E viruses at the P1/P2 junction indicating that these viruses may be reclassified as a single highly diverse species. Based on genetic distance criteria for assigning genotypes corresponding to neutralization serotypes in enteroviruses we identified 26 new HCoSV genotypes belonging to species A, D, and E. The detection of a large number of HCoSV genotypes based on still limited geographic sampling indicates that the phenotypic effects of cosaviruses on infected subjects are likely to be as highly diverse as those of human enteroviruses.

The frequent interactions of rodents with humans make them a common source of zoonotic infections. To obtain an initial unbiased measure of the viral diversity in the enteric tract of wild rodents we sequenced partially purified, randomly amplified viral RNA and DNA in the feces of 105 wild rodents (mouse, vole, and rat) collected in California and Virginia. We identified in decreasing frequency sequences related to the mammalian viruses families Circoviridae, Picobirnaviridae, Picornaviridae, Astroviridae, Parvoviridae, Papillomaviridae, Adenoviridae, and Coronaviridae. Seventeen small circular DNA genomes containing one or two replicase genes distantly related to the Circoviridae representing several potentially new viral families were characterized. In the Picornaviridae family two new candidate genera as well as a close genetic relative of the human pathogen Aichi virus were characterized. Fragments of the first mouse sapelovirus and picobirnaviruses were identified and the first murine astrovirus genome was characterized. A mouse papillomavirus genome and fragments of a novel adenovirus and adenovirus-associated virus were also sequenced. The next largest fraction of the rodent fecal virome was related to insect viruses of the Densoviridae, Iridoviridae, Polydnaviridae, Dicistroviriade, Bromoviridae, and Virgaviridae families followed by plant virus-related sequences in the Nanoviridae, Geminiviridae, Phycodnaviridae, Secoviridae, Partitiviridae, Tymoviridae, Alphaflexiviridae, and Tombusviridae families reflecting the largely insect and plant rodent diet. Phylogenetic analyses of full and partial viral genomes therefore revealed many previously unreported viral species, genera, and families. The close genetic similarities noted between some rodent and human viruses might reflect past zoonoses. This study increases our understanding of the viral diversity in wild rodents and highlights the large number of still uncharacterized viruses in mammals.

BackgroundStool consistency is an important diagnostic criterion in both research and clinical medicine and is often used to define diarrheal disease.MethodsWe examine the pediatric enteric virome across stool consistencies to evaluate differences in richness and community composition using fecal samples collected from children aged 0 to 5 years participating in a clinical trial in the Amhara region of Ethiopia. The consistency of each sample was graded according to the modified Bristol Stool Form Scale for children (mBSFS-C) before a portion of stool was preserved for viral metagenomic analysis. Stool samples were grouped into 29 pools according to stool consistency type. Differential abundance was determined using negative-binomial modeling.ResultsOf 446 censused children who were eligible to participate, 317 presented for the study visit examination and 269 provided stool samples. The median age of children with stool samples was 36 months. Species richness was highest in watery-consistency stool and decreased as stool consistency became firmer (Spearman's r = - 0.45, p = 0.013). The greatest differential abundance comparing loose or watery to formed stool was for norovirus GII (7.64, 95% CI 5.8, 9.5) followed by aichivirus A (5.93, 95% CI 4.0, 7.89) and adeno-associated virus 2 (5.81, 95%CI 3.9, 7.7).ConclusionsIn conclusion, we documented a difference in pediatric enteric viromes according to mBSFS-C stool consistency category, both in species richness and composition.

ObjectivesWe examined the fecal virome and bacterial community composition of children with Crohn disease (CD), ulcerative colitis (UC), and healthy controls to test the hypothesis that unique patterns of viral organisms and/or presence of bacterial pathogens may be identified that could contribute to the pathogenesis of pediatric inflammatory bowel disease (IBD).MethodsFecal samples from 24 children (mean 12.2 years) with CD (n = 7) or UC (n = 5) and similar aged controls (n = 12) were processed to determine individual viromes. Viral sequences were identified through translated protein sequence similarity search. Bacterial microbiota were determined by sequencing of the V4 region of the 16S rRNA gene.ResultsOnly a few human viruses were detected, so virome analyses focused on bacterial viruses. The relative abundance of Caudovirales was greater than that of Microviridae phages in both IBD and healthy controls. Caudovirales phages were more abundant in CD (mean 80.8%) than UC (48.8%) (P = 0.05) but not controls. The richness of viral strains in Microviridae but not Caudovirales was higher in controls than CD (P = 0.05) but not UC cases. No other measure of phage abundance, richness, or Shannon diversity showed significant difference between the 2 IBD and control groups. Bacterial microbiota analysis revealed that IBD diagnosis, albumin, hemoglobin, erythrocyte sedimentation rate, and probiotic supplementation correlated to the composition of gut bacterial microbiota.ConclusionsMinor patterns in gut virome and bacterial community composition distinguish pediatric IBD patients from healthy controls. Probiotics are associated with bacterial microbiota composition. These exploratory results need confirmation in larger studies.

BACKGROUND:The enteric viruses shed by different populations can be influenced by multiple factors including access to clean drinking water. We describe here the eukaryotic viral genomes in the feces of Ethiopian children participating in a clean water intervention trial. METHODOLOGY/PRINCIPAL FINDINGS:Fecal samples from 269 children with a mean age of 2.7 years were collected from 14 villages in the Amhara region of Ethiopia, half of which received a new hand-dug water well. Feces from these villages were then analyzed in 29 sample pools using viral metagenomics. A total of 127 different viruses belonging to 3 RNA and 3 DNA viral families were detected. Picornaviridae family sequence reads were the most commonly found, originating from 14 enterovirus and 6 parechovirus genotypes plus multiple members of four other picornavirus genera (cosaviruses, saliviruses, kobuviruses, and hepatoviruses). Picornaviruses with nearly identical capsid VP1 were detected in different pools reflecting recent spread of these viral strains. Next in read frequencies and positive pools were sequences from the Caliciviridae family including noroviruses GI and GII and sapoviruses. DNA viruses from multiple genera of the Parvoviridae family were detected (bocaviruses 1-4, bufavirus 3, and dependoparvoviruses), together with four species of adenoviruses and common anelloviruses shedding. RNA in the order Picornavirales and CRESS-DNA viral genomes, possibly originating from intestinal parasites or dietary sources, were also characterized. No significant difference was observed between the number of mammalian viruses shed from children from villages with and without a new water well. CONCLUSIONS:We describe an approach to estimate the efficacy of potentially virus transmission-reducing interventions and the first complete (DNA and RNA viruses) description of the enteric viromes of East African children. A wide diversity of human enteric viruses was found in both intervention and control groups. Mammalian enteric virome diversity was not reduced in children from villages with a new water well. This population-based sampling also provides a baseline of the enteric viruses present in Northern Ethiopia against which to compare future viromes.

Parvoviruses are small icosahedral viruses with linear single-stranded DNA genomes of ~5 kb that are associated with a wide spectrum of illnesses in humans and animals. The subfamily Parvovirinae, which [...]

To the Editor: For nearly 3 decades, human parvovirus B19 (B19V) was considered to be the only pathogenic parvovirus found in humans. Since 2005, several new human parvoviruses have been [...]

Bathymetry data is indispensable for a variety of aquatic field studies and benthic resource inventories. Determining water depth can be accomplished through an echo sounding system or remote estimation utilizing space-borne and air-borne data across diverse environments, such as lakes, rivers, seas, or lagoons. Despite being a common option for bathymetry mapping, the use of satellite imagery faces challenges due to the complex inherent optical properties of water bodies (e.g., turbid water), satellite spatial resolution limitations, and constraints in the performance of retrieval models. This study focuses on advancing the remote sensing based method by harnessing the non-linear learning capabilities of the machine learning (ML) model, employing advanced feature selection through a meta-heuristic algorithm, and using image extraction techniques (i.e., band ratio, gray scale morphological operation, and morphological multi-scale decomposition). Herein, we validate the predictive capabilities of six ML models: Random Forest (RF), Support Vector Machine (SVM), CatBoost (CB), Extreme Gradient Boost (XGB), Light Gradient Boosting Machine (LGBM), and KTBoost (KTB) models, both with and without the application of meta-heuristic optimization (i.e., Dragon Fly, Particle Swarm Optimization, and Grey Wolf Optimization), to accurately ascertain water depth. This is achieved using a diverse input dataset derived from multi-spectral Landsat 9 imagery captured on a cloud-free day (19 September 2023) in a shallow, turbid lagoon. Our findings indicate the superior performance of LGBM coupled with Particle Swamp Optimization (R2 = 0.908, RMSE = 0.31 m), affirming the consistency and reliability of the feature extraction and selection-based framework, while offering novel insights into the expansion of bathymetric mapping in complex aquatic environments.

Soil Organic Carbon (SOC) influences many soil properties including nutrient and water holding capacity, nutrient cycling and stability, improved water infiltration and aeration. It also is an essential parameter in the assessment of soil quality, especially for agricultural production. However, SOC mapping is a complicated process that is costly and time-consuming due to the physical challenges of the natural conditions that is being surveyed. The best model for SOC mapping is still in debate among many researchers. Recently, the development of machine learning and Geographical Information Systems (GIS) has provided the potential for more accurate spatial prediction of SOC content. This research was conducted in a relatively small-scale capacity in the Central Vietnam region. The aim of this study is to compare the accuracy of Inverse Distance Weighting (IDW), Ordinary Kriging (OK), and Random Forest (RF) methods for SOC interpolation, with a dataset of 47 soil samples for an area of 145 hectares. Three environmental variables including elevation, slope, and the Normalized Difference Vegetation Index (NDVI) were used for the RF model. In the RF model, the values of the number of variables randomly sampled as candidates at each split, (mtry), and the number of bootstrap replicates, (ntree), were determined in terms of 1 and 1,000 respectively The results at our research site showed that using IDW is the most accurate method for SOC mapping, followed by the methods of RF and OK respectively. Concerning SOC mapping based-on auxiliary variables, in areas where there is human activity, the selection of auxiliary variables should be carefully considered because the variation in the SOC may not only be due to environmental variables but also by farming technologies.

In recent years, water for agricultural production gradually became a significant challenge in the context of climate change in Vietnam. Sustainable solutions are required, which consider the use of resources for both human needs and ecology, and that account for the equitable distribution and the livelihood of the farmers now and in the future. In particular, the farmers in the province of Quang Nam facing water shortage in the cultivation of paddy in the summer-autumn season. Conflicts arise regarding the sharing of the water between the farmers, the drinking water company and the hydropower company. In the context of climate change, the water shortage is expected to increase in the future. The article presents the results of participatory action research (PAR) approach to develop a local level mechanism for water sharing, in which stakeholders actively participated. Water sharing mechanism was developed, envisioning a sustainable solution for inclusive water sharing. The mechanism was successfully implemented in two cases, one at commune level (Tho stream) and one at the district level (Mo stream). The participatory approach proved to be successful in setting up a broadly acceptable mechanism that will need to be further incorporated in the institutional set-up. Keywords: Adaptation, Agriculture, Climate change, Governance, Rice production, Water sharing

In recent years, both scientists and local governments have been giving serious attention to land evaluation, especially in regard to the use of agricultural land. This is with the intention of increasing the sustainability of agricultural production. In Vietnam, acacia plantations play an important role in the livelihoods of farmers in mountainous regions. Therefore, identifying suitable areas for acacia plantations is an important consideration within mountainous areas. This research was conducted in Nam Dong district, Central Vietnam, using six physical soil criteria for land evaluation by the Analytic Hierarchy Process (AHP) and also the Fuzzy Analytic Hierarchy Process (FAHP). The results have shown that the ranking of selected criteria in both methods was the same, but the weighting of each criterion was different. Among the six physical soil criteria, soil depth has the highest priority, followed by slope, soil organic carbon content, soil texture, soil pH, and soil type. The suitability maps for acacia plantations within the area studied have shown that 9344 ha were not suitable, and 99 ha had low suitability for acacia plantation by both methods. For the AHP approach, 928 hectares were in the range of moderate suitability, and 3080 hectares were in the high suitability class. In contrast, the FAHP method determined 905 hectares to be of the moderate suitability class and 3102 hectares to be of the high suitability class. Based on the observed acacia’s productivity and the scores of the two methods, it shows that the FAHP has a stronger correlation than the of AHP. Within the six selected criteria, the FAHP method can increase the accuracy of land evaluation results by 4.62% in comparison to the original AHP method. Therefore, the FAHP is the most suitable method for land evaluation, especially for agricultural land planning. Further studies should be integrated into more social and economic criteria for comprehensive land evaluation scenarios.

Soil quality assessment is valuable for agricultural production. In this research, 155 soil samples at two soil depths were collected from four land use types in an agricultural area of the A Luoi district in the Central Vietnam. Differences of soil organic carbon, total nitrogen in soil and soil pH under different land use types and topographic aspects were compared. Soil organic carbon contents in arable land and plantation forest are higher than those in natural forest and grassland (p

Even though indigenous knowledge (IK) is considered as one of the most effective strategies in response to climate change issues, this form is not being sufficiently integrated into the climate change planning and policy at both local and national levels in Vietnam. This study investigates the role of the traditional agricultural practices of the Xo Dang ethnic minority groups in Central Vietnam and provides insights into the factors that influence farmers to adopt these practices in response to climate change. Primary data was obtained through three focus group discussions and 87 household surveys involving the Xo Dang people through face-to-face semi-structured interviews in the Tra Doc commune, Bac Tra My district, Quang Nam province, Central Vietnam. The binary logistic regression model was used to examine the factors which have influenced the choices made by this community in response to climate change. The results showed that Xo Dang people were highly aware of climate change risks and had, in response, employed their current adaptation practices. The major adaptation strategies implemented by the Xo Dang people included the use of flora and fauna indicators, native plant varieties, the adjustment of planting calendars, irrigation practices, and the application of intercropping. The results indicated that the living years, their monthly farm incomes, and farmer's perceptions of ongoing climate change effects on their environment were the factors that significantly affected farmers' adaptation decisions. Understanding indigenous knowledge plays a fundamental role in the processes of deciding the appropriate adaptation techniques more effectively and making use of human resources. Therefore, policy makers should pay much attention to indigenous knowledge to combat climate change in future national policies and projects.

Central Vietnam is very susceptible to soil erosion due to its complicated terrain and heavy rainfall. The objective of this study was to quantify soil erosion in the A Sap river basin, A Luoi district, Thua Thien Hue Province, Vietnam, using the Universal Soil Loss Equation (USLE) and Geographical Information System (GIS). The results showed that 34% of land area lost accumulated to 10 t ha−1 year−1 while 47% of the total area lost less than 1 t ha−1 year−1. Natural forest land lost the most with an average of about 19 t ha−1 year−1, followed by plantation forest with approximately 7 t ha−1 year−1 and other agricultural lands at 3.70 and 1.45 t ha−1 year−1 for yearly crops and paddy rice, respectively. Soil erosion was most sensitive to the topographic factor (LS), followed by the practice support factor (P), soil erodibility factor (K), cropping management (C), and the rainfall erosivity factor (R). Implications are that changes to the cultivated calendar and implementing intercropping are effective ways to prevent soil erosion in cultivated lands. Furthermore, introducing broad leaves trees for mountainous areas in A Sap basin was the most effective practice in reducing soil erosion. The study also pointed out that the combination of available data sources used with the USLE and GIS technology is a viable option to calculate soil erosion in Central Vietnam, which would allow targeted attention toward a solution is to reduce future soil erosion. Keywords: Central Vietnam, GIS, Soil erosion, USLE

A large, highly prolific swine farm in Hungary had a 2-year history of neurologic disease among newly weaned (25- to 35-day-old) pigs, with clinical signs of posterior paraplegia and a high mortality rate. Affected pigs that were necropsied had encephalomyelitis and neural necrosis. Porcine astrovirus type 3 was identified by reverse transcription PCR and in situ hybridization in brain and spinal cord samples in 6 animals from this farm. Among tissues tested by quantitative RT-PCR, the highest viral loads were detected in brain stem and spinal cord. Similar porcine astrovirus type 3 was also detected in archived brain and spinal cord samples from another 2 geographically distant farms. Viral RNA was predominantly restricted to neurons, particularly in the brain stem, cerebellum (Purkinje cells), and cervical spinal cord. Astrovirus was generally undetectable in feces but present in respiratory samples, indicating a possible respiratory infection. Astrovirus could cause common, neuroinvasive epidemic disease.