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Background: The causative agents of Acute Encephalitis Syndrome remain unknown in 68–75% of the cases. In Nepal, the cases are tested only for Japanese encephalitis, which constitutes only about 15% of the cases. However, there could be several organisms, including vaccine-preventable etiologies that cause acute encephalitis, when identified could direct public health efforts for prevention, including addressing gaps in vaccine coverage. Objectives: This study employs metagenomic next-generation-sequencing in the investigation of underlying causative etiologies contributing to acute encephalitis syndrome in Nepal. Methods: In this study, we investigated 90, Japanese-encephalitis-negative, banked cerebrospinal fluid samples that were collected as part of a national surveillance network in 2016 and 2017. Randomization was done to include three age groups (< 5-years; 5-14-years; >15-years). Only some metadata (age and gender) were available. The investigation was performed in two batches which included total nucleic-acid extraction, followed by individual library preparation (DNA and RNA) and sequencing on Illumina iSeq100. The genomic data were interpreted using Chan Zuckerberg-ID and confirmed with polymerase-chain-reaction. Results: Human-alphaherpes-virus 2 and Enterovirus-B were seen in two samples. These hits were confirmed by qPCR and semi-nested PCR respectively. Most of the other samples were marred by low abundance of pathogen, possible freeze-thaw cycles, lack of process controls and associated clinical metadata. Conclusion: From this study, two documented causative agents were revealed through metagenomic next-generation-sequencing. Insufficiency of clinical metadata, process controls, low pathogen abundance and absence of standard procedures to collect and store samples in nucleic-acid protectants could have impeded the study and incorporated ambiguity while correlating the identified hits to infection. Therefore, there is need of standardized procedures for sample collection, inclusion of process controls and clinical metadata. Despite challenging conditions, this study highlights the usefulness of mNGS to investigate diseases with unknown etiologies and guide development of adequate clinical-management-algorithms and outbreak investigations in Nepal. [ABSTRACT FROM AUTHOR]

Background: Environmental surveillance, using detection of Salmonella Typhi DNA, has emerged as a potentially useful tool to identify typhoid-endemic settings; however, it is relatively costly and requires molecular diagnostic capacity. We sought to determine whether S. Typhi bacteriophages are abundant in water sources in a typhoid-endemic setting, using low-cost assays. Methodology: We collected drinking and surface water samples from urban, peri-urban and rural areas in 4 regions of Nepal. We performed a double agar overlay with S. Typhi to assess the presence of bacteriophages. We isolated and tested phages against multiple strains to assess their host range. We performed whole genome sequencing of isolated phages, and generated phylogenies using conserved genes. Findings: S. Typhi-specific bacteriophages were detected in 54.9% (198/361) of river and 6.3% (1/16) drinking water samples from the Kathmandu Valley and Kavrepalanchok. Water samples collected within or downstream of population-dense areas were more likely to be positive (72.6%, 193/266) than those collected upstream from population centers (5.3%, 5/95) (p=0.005). In urban Biratnagar and rural Dolakha, where typhoid incidence is low, only 6.7% (1/15, Biratnagar) and 0% (0/16, Dolakha) river water samples contained phages. All S. Typhi phages were unable to infect other Salmonella and non-Salmonella strains, nor a Vi-knockout S. Typhi strain. Representative strains from S. Typhi lineages were variably susceptible to the isolated phages. Phylogenetic analysis showed that S. Typhi phages belonged to the class Caudoviricetes and clustered in three distinct groups. Conclusions: S. Typhi bacteriophages were highly abundant in surface waters of typhoid-endemic communities but rarely detected in low typhoid burden communities. Bacteriophages recovered were specific for S. Typhi and required Vi polysaccharide for infection. Screening small volumes of water with simple, low-cost (~$2) plaque assays enables detection of S. Typhi phages and should be further evaluated as a scalable tool for typhoid environmental surveillance. Author summary: Typhoid fever is a major health issue in low- and middle-income countries, causing illness and death. The World Health Organization recommends the use of typhoid-conjugate vaccines to combat its spread. However, limited data on typhoid prevalence in these countries hinders effective vaccination programs. Environmental surveillance, which involves detecting Salmonella Typhi DNA in the environment, has emerged as a method to identify high-risk areas for typhoid transmission. Nevertheless, this approach is costly and requires infrastructure often unavailable in many communities. To address this, we conducted a study in Nepal to explore a low-cost and sustainable typhoid surveillance method. We examined typhoid bacteriophages in surface and drinking water across communities with varying population densities and typhoid burdens. Phages were easily detectable in communities with high typhoid burdens but less prevalent in areas with lower burdens. The isolated phages exhibited specificity for S. Typhi and were effective against different bacterial strains in Nepal. This study demonstrates that phage-based assays can be a simple and affordable tool for typhoid environmental surveillance. This method can help identify areas that require vaccination prioritization and interventions for clean water and sanitation. By utilizing phage-based assays, health authorities can better understand typhoid transmission and implement targeted control measures. [ABSTRACT FROM AUTHOR]

Nepal initiated numerous hydropower and irrigation‐related infrastructure projects to enhance and promote green energy, water security, and agricultural productivity. However, these projects may pose risks to natural habitats and the well‐being of aquatic fauna, leading to significant effects on delicate ecosystems. To understand these potential impacts, it is crucial to gather reliable baseline data on the population status and habitat characteristics of species. This study specifically focuses on Gharials (Gavialis gangeticus), a critically endangered species. We recorded data on pre‐determined habitat variables at stations spaced 500 m apart along the two major river streams of Bardia National Park, as well as at locations where Gharials were sighted between February and March 2023. We used binary logistic regression with a logit link function to investigate the habitat characteristics related to the occurrence of Gharials. The presence/absence of Gharials at sampling points served as the dependent variable, while 10 other predetermined variables (ecological variables and disturbance variables) served as independent variables. Our study recorded 23 Gharials, comprising 14 adults, six sub‐adults, and three juveniles, with a sex ratio of 55.56 males per 100 females. Most individuals (83%) were found basking. Among the 10 habitat predictors, three variables (mid‐river depth, river width, and water temperature) were significantly correlated (p <.05) with the probability of Gharial occurrence. The model shows that Gharial detection probability increases with greater mid‐river depth and width and lower water temperature. This study establishes a population baseline for Gharials within the river system before the construction of large infrastructure projects, such as dams and irrigation canals. It also recommends continuous monitoring of Gharial populations after water release and/or diversion to evaluate the impact of large infrastructure projects on the population and their associated habitat characteristics. This will help enable more informed and targeted conservation efforts. [ABSTRACT FROM AUTHOR]

Introduction: Salmonella Typhi and Salmonella Paratyphi, fecal-oral transmitted bacterium, have temporally and geographically heterogeneous pathways of transmission. Previous work in Kathmandu, Nepal implicated stone waterspouts as a dominant transmission pathway after 77% of samples tested positive for Salmonella Typhi and 70% for Salmonella Paratyphi. Due to a falling water table, these spouts no longer provide drinking water, but typhoid fever persists, and the question of the disease's dominant pathway of transmission remains unanswered. Methods: We used environmental surveillance to detect Salmonella Typhi and Salmonella Paratyphi A DNA from potential sources of transmission. We collected 370, 1L drinking water samples from a population-based random sample of households in the Kathmandu and Kavre Districts of Nepal between February and October 2019. Between November 2019 and July 2021, we collected 380, 50mL river water samples from 19 sentinel sites on a monthly interval along the rivers leading through the Kathmandu and Kavre Districts. We processed drinking water samples using a single qPCR and processed river water samples using differential centrifugation and qPCR at 0 and after 16 hours of liquid culture enrichment. A 3-cycle threshold (Ct) decrease of Salmonella Typhi or Salmonella Paratyphi, pre- and post-enrichment, was used as evidence of growth. We also performed structured observations of human-environment interactions to understand pathways of potential exposure. Results: Among 370 drinking water samples, Salmonella Typhi was detected in 7 samples (1.8%) and Salmonella Paratyphi A was detected in 4 (1.0%) samples. Among 380 river water samples, Salmonella Typhi was detected in 171 (45%) and Salmonella Paratyphi A was detected in 152 (42%) samples. Samples located upstream of the Kathmandu city center were positive for Salmonella Typhi 12% of the time while samples from locations in and downstream were positive 58% and 67% of the time respectively. Individuals were observed bathing, washing clothes, and washing vegetables in the rivers. Implications: These results suggest that drinking water was not the dominant pathway of transmission of Salmonella Typhi and Salmonella Paratyphi A in the Kathmandu Valley in 2019. The high degree of river water contamination and its use for washing vegetables raises the possibility that river systems represent an important source of typhoid exposure in Kathmandu. Author summary: Understanding the dominant route of transmission of a pathogen is important for designing and implementing effective control strategies. Salmonella Typhi and Paratyphi A, which cause enteric fever, infect approximately 10 million people and cause over 100,000 deaths annually. In the Kathmandu Valley, prior work suggested ancient stone spouts used for drinking water were often contaminated and driving transmission of the diseases. However, many of these spouts no longer function, and people are still getting sick, suggesting other possible dominant pathways for enteric fever transmission. We tested drinking water from households in this area as well as local river water and found that only 7 drinking water samples were positive for Salmonella Typhi and 4 were positive for Salmonella Paratyphi A. We also tested river water and found many samples (>40%) tested positive for these bacteria. River water samples were not often positive upstream of Kathmandu city center (12% positive for Salmonella Typhi) but were often positive within the city center (58% positive for Salmonella Typhi) and in rural areas up to 10 km downstream of the city (67% positive for Salmonella Typhi). During sample collection, individuals were observed interacting with rivers by walking in them, washing clothes and washing vegetables for sale in markets. This study shows that drinking water may not be a primary driver of enteric fever transmission in the Kathmandu Valley, but that sewage contaminated river water may be a way disease transmits into the wider population. [ABSTRACT FROM AUTHOR]

Introduction COVID-19 pandemic has challenged the health system globally specially the low to middle income countries. Renal transplant recipient is at risk due to immunosuppressed state. The course of the disease and its outcome is not completely known and there is scarcity of information from developing world. Methods The study was carried out at Tribhuvan University Teaching Hospital, Kathmandu from May 2020 till May 2021. All of the renal transplant recipients infected with COVID-19 virus were included in the study. Duration of transplantation, recipient’s comorbidities, clinical presentation including laboratory investigations and outcome in terms of hospitalization, need of intensive care, and need of mechanical ventilation, organ failure and mortality were studied. Results There were 71 patients (male/female: 60/11, mean age 42.6±10.4) were included in the study. 72% patients (n=51) required hospitalization. There were 15 patients (21%) who expired. Patients requiring mechanical ventilation were 14 (19.7%), 24 (33.8%) required intensive care, 10 (14%) required hemodialysis support during admission. A prior history of rejection, presence of diabetes, graft dysfunction at baseline, and a higher creatinine at baseline was associated with mortality. Hypoxia, leucopenia, lymphopenia was predictive with mortality. Raised inflammatory markers as d-Dimer, LDH, development of acute kidney injury was associated with mortality. Presence of acute kidney injury was associated with increased risk of mortality, need of intensive care and prolonged hospitalizations. Conclusion COVID-19 infection in renal transplant recipients carries a high risk for mortality. The factors that correlated with risk for mortality were hypoxia, leucopenia, high inflammatory markers and need of mechanical ventilation. [ABSTRACT FROM AUTHOR]

Introduction Transplant renal artery stenosis (TRAS) is the most common preventable vascular complication in kidney transplantation with significant rates of graft loss and mortality. We aimed to study the demographics, prevalence, clinical presentation, and outcome of TRAS. Methods We retrospectively reviewed medical records of all living donor kidney transplant recipients at Tribhuvan University Teaching Hospital from August 2008 to May 2021. Cases diagnosed with TRAS by ultrasound Doppler and/or renal CT angiogram were included. Data on demographics, clinical presentation, management, and outcomes were collected and analyzed. Among patients who underwent revascularization, pre and post-procedure creatinine, blood pressure (BP), and antihypertensive medicine burden were compared. Results Among 620 living donor kidney transplantation, TRAS was present in 17 recipients (Male:Female = 16:1) (2.6%); mean age was 35.47±12.71 years. The median duration at diagnosis was onemonth post-transplant (range: 5 days-9 months). The most common clinical features of TRAS were graft dysfunction and uncontrolled hypertension. Diagnosis of TRAS was confirmed with CT angiography in 13 patients. Ten patients underwent revascularization. Pre and post-revascularization mean serum creatinine was 356±210.49 µmol/L and 122.8±30.48 µmol/L (p=0.007) respectively, mean systolic BP was 200±12.47 mmHg and 133±13.38 mmHg (p=0.005) respectively and mean diastolic BP was 105±15.09 mmHg and 80±9.43 mmHg(p=0.005) respectively. Significant reduction in antihypertensive pill burden was achieved. Conclusion Prevalence of TRAS was 2.6%. Most cases presented early with hypertension and graft dysfunction. Revascularization of significant stenosis had a favorable outcome in terms of BP control, antihypertensive pill burden, and preservation of renal function. [ABSTRACT FROM AUTHOR]

Nepal is a global biodiversity hotspot, supporting 213 mammal species with diverse habitats across various landscape types, from the lowland Terai to the high Himalayas. Studies of Nepal's mammalian fauna are not evenly distributed and better understanding of past biases towards some species, research themes and locations can provide better strategic direction for future research investments. Therefore, we reviewed 575 scientific articles on mammals in Nepal, published between 2000 and 2019 and compiled these in March 2020, to examine trends, patterns and gaps, and pave future plans for mammalian research in Nepal. A positive increase in the number of publications (β = 0.27 ± 0.02SD, P < 0.00) was observed, with a more than threefold increase between 2010 and 2019 compared to 2000–2009 (t = − 6.26, df = 12.21, P < 0.000). Analysis of these documents revealed that mammalian researches favored large flagship, threatened species of carnivores inside Nepal's protected area system. Geographically, mammalian research was not uniform in Nepal, as most studies were concentrated in Bagmati Province and in the Terai and Chure region. Baseline surveys and ecological studies were more common types of research, while studies on the impact of climate change and wildlife trade and poaching, are scant, which deserves a future look. While these studies shape current mammalogy in Nepal, studies of small, uncharismatic species, and in areas outside protected areas and other provinces except Bagmati, Lumbini and Province One are severely lacking. The research identified habitat loss, degradation and human-wildlife conflict as the major threats to the survival of mammalian species in Nepal. Therefore, redesigning and strict implementation of policies based on habitat management and human-wildlife co-existence, including other threat mitigation measures, are warranted. To address knowledge gaps, the prioritization of future research and funding should be focused on relatively unexplored research themes and under-researched provinces. This approach will help to re-align the research focus with the current need, and assist to fully understand and effectively conserve the wealth of mammalian diversity that Nepal holds. [ABSTRACT FROM AUTHOR]

Background: Medical students and residents were found to have suffered from depression, anxiety, and burnout in various studies. However, these entities have not been adequately explored in the context of Nepal. We proposed to determine the prevalence of depression, anxiety, burnout, their associated factors, and identify their predictors in a sample of medical students and residents in a Nepalese medical school. Methods: It was a cross-sectional study with 651 medical students and residents chosen at random between December 2018 and February 2019. The validated Nepali version of Hospital Anxiety and Depression Scale, the Copenhagen Burnout Inventory, and Medical Students' Stressor Questionnaire were used to assess depression, anxiety, burnout, and stressors respectively. We used univariate and multivariable logistic regression analyses to identify the correlation of predictor variables with depression, anxiety, and burnout. Results: The overall prevalence of burnout (48.8%; 95% CI 44.9–52.7) and anxiety (45.3%; 95% CI 41.4–49.2) was more than that of depression (31%; 95% CI 27.5–34.7). Burnout and depression were more prevalent in residents than in medical students (burnout: 64.5% vs 37.6%, P-value < 0.0001; depression: 33.7% vs 29.1%, P-value 0.21). Whereas, medical students were found more anxious than residents (46.3% versus 43.96%, P-value 0.55). Academic related stressors caused high-grade stress to participants. Multivariable model for depression significantly showed anxiety, personal burnout, and work-related burnout as risk enhancing correlates; satisfaction with academic performance as a protective correlate. Similarly, the multivariate model for anxiety significantly identified female gender, depression, personal burnout, teaching and learning related stressors, and past history of mental illness as risk enhancing correlates; being satisfied with academic performance, getting adequate sleep, and being a second-year resident as protective correlates. The logistic model for burnout significantly showed being a first-year resident, depression, anxiety, and drive and desire related stressors as positive predictors. None of the variables were identified as significant negative predictors of burnout. Conclusions: A high prevalence of depression, anxiety, and burnout was seen among medical students and residents. Most of them were stressed with academic-related factors. A strong correlation between teaching and learning-related stressors with depression and anxiety may be a call for an efficient and more student-friendly curriculum. [ABSTRACT FROM AUTHOR]

Creutzfeldt‐Jakob disease (CJD) can also be diagnosed in a resource‐limited setting through good clinical analysis. The diagnosis of CJD should be considered in patients with rapidly evolving neurological signs associated with cognitive disturbances even in countries with limited available sophisticated tools and where CJD was never reported before. [ABSTRACT FROM AUTHOR]

Intraguild interactions have important implications for carnivore demography and conservation. Differences in how predators respond to different forms of disturbance might alter their interaction patterns. We sought to understand how human and livestock disturbance impact co-occurrence of sympatric large carnivores such as tiger (Panthera tigris) and leopard (P. pardus) and thereby mediate the intraguild interaction pattern to enable coexistence of the species in a human-dominated landscape. We surveyed 361 locations in Chitwan National Park, Nepal, to examine how prey abundance and disturbance factors such as human and livestock presence might influence habitat use by tigers and leopards independently and when co-occurring. Single-species single-season models and two-species single-season models were developed to examine hypotheses on unconditional detection and occupancy and species interaction respectively. Pervasive human use of the park had negative impacts on tiger occupancy while the abundance of prey had a positive influence. Despite significant prey overlap between tigers and leopards, none of the native prey species predicted leopard habitat occupancy. However, habitats used extensively by livestock were also used by leopards. Further, we found strong evidence of intraguild competition. For instance tiger occupancy was higher in prey-rich areas and leopard occupancy was low in the sites where tigers were present. These findings, and a species interaction factor of < 1 clearly indicate that leopards avoid tigers, but their use of areas of disturbance enables them to persist in fringe habitats. We provide empirical evidence of how intraguild interaction may result in habitat segregation between competing carnivores, while also showing that human and livestock use of the landscape create disturbance patterns that facilitate co-occurrence of the predators. Thus, because large carnivores compete, some disturbance may mediate coexistence in small protected areas. Understanding such interactions can help address important conservation challenges associated with maintaining diverse carnivore communities in small or disturbed landscapes. [ABSTRACT FROM AUTHOR]

Correction to: Patterns and trends in two decades of research on Nepal's mammalian fauna (2000-2019): examining the past for future implications The correct name should read Nishan K.C The original article has been corrected. Correction to: Biodiversity and Conservation https://doi.org/10.1007/s10531-021-02289-2 In the original publication of the article two errors have been identified which are as follows: The affiliation of Karan Shah has been shown from 1,2,3,4,5,6,7,8,9 but his affiliation is only 9 i.e. Himalayan Nature, Kathmandu, Nepal. [Extracted from the article]

Measures of absolute animal abundance may be estimated by capture-recapture, removal, or distance sampling methods. We investigate the usage of binomial mixture models to estimate local group abundance of major prey species that is frequently used as a surrogate for prey abundance to study predator or prey-mediated ecological interactions such as predator-prey relationships. We evaluate mixture models using data from a camera-trapping survey intended for a tiger Panthera tigris census in Chitwan National Park, Nepal, where the entire park was surveyed in 361 4-km2 quadrats. We chose four prey species (chital Axis axis, sambar Rusa unicolor, muntjac Muntiacus muntjac, and wild boar Sus scrofa) that collectively account for > 75% of prey biomass consumed by tigers. Abundance of prey group was modeled as a random variable with a Poisson or a negative binomial distribution, with the mean abundance affected by distance from water sources, elevation, and normalized difference vegetation index (NDVI). Except for wild boar, the top models for all other species included the hypothesized covariates while the null model was the most parsimonious model for the wild boar. The most parsimonious chital model included effects of distance from water sources (−) and elevation (−). The sambar model supported all three covariates: distance from water sources (−), elevation (+), and NDVI (+). Only distance from water sources (−) was supported by the most parsimonious muntjac model. Our abundance estimates also conformed to the results obtained from recently conducted labor-intensive distance sampling procedure. We conclude that camera-trapping survey data can be effectively utilized adopting the binomial mixture model framework to understand animal abundance-habitat relationships and estimate abundance of animal that are not identifiable individually. [ABSTRACT FROM AUTHOR]