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A patient with fever presented to the referral infectious disease hospital in Kathmandu, Nepal. Metagenomic sequencing of the patient's serum recovered a near-complete genome of human immunodeficiency virus-1 (HIV-1), distinct from previous HIV-1 genomes from Nepal in GenBank. It shared 92.48% nucleotide identity with an HIV-1 subtype C isolate from India., Competing Interests: The authors declare no conflict of interest.

Background: The 4 serotypes of dengue virus (DENV1-4) can each cause potentially deadly dengue disease, and are spreading globally from tropical and subtropical areas to more temperate ones. Nepal provides a microcosm of this global phenomenon, having met each of these grim benchmarks. To better understand DENV transmission dynamics and spread into new areas, we chose to study dengue in Nepal and, in so doing, to build the onsite infrastructure needed to manage future, larger studies., Methods and Results: During the 2022 dengue season, we enrolled 384 patients presenting at a hospital in Kathmandu with dengue-like symptoms; 79% of the study participants had active or recent DENV infection (NS1 antigen and IgM). To identify circulating serotypes, we screened serum from 50 of the NS1 + participants by RT-PCR and identified DENV1, 2, and 3 - with DENV1 and 3 codominant. We also performed whole-genome sequencing of DENV, for the first time in Nepal, using our new on-site capacity. Sequencing analysis demonstrated the DENV1 and 3 genomes clustered with sequences reported from India in 2019, and the DENV2 genome clustered with a sequence reported from China in 2018., Conclusion: These findings highlight DENV's geographic expansion from neighboring countries, identify China and India as the likely origin of the 2022 DENV cases in Nepal, and demonstrate the feasibility of building onsite capacity for more rapid genomic surveillance of circulating DENV. These ongoing efforts promise to protect populations in Nepal and beyond by informing the development and deployment of DENV drugs and vaccines in real time., (© 2024. The Author(s).)

Acute encephalitis syndrome (AES) causes significant morbidity and mortality worldwide. In Nepal, Japanese encephalitis virus (JEV) accounts for ~5-20% of AES cases, but ~75% of AES cases are of unknown etiology. We identified a gemykibivirus in CSF collected in 2020 from an 8-year-old male patient with AES using metagenomic next-generation sequencing. Gemykibiviruses are single stranded, circular DNA viruses in the family Genomoviridae . The complete genome of 2,211 nucleotides was sequenced, which shared 98.69% nucleotide identity to its closest relative, Human associated gemykibivirus 2 isolate SAfia-449D. Two real-time PCR assays were designed, and screening of 337 cerebrospinal fluid (CSF) and 164 serum samples from AES patients in Nepal collected in 2020 and 2022 yielded 11 CSF and 1 serum sample that were positive in both PCR assays. Complete genomes of seven of the positives were sequenced. These results identify a potential candidate etiologic agent of encephalitis in Nepal., Importance: Viral encephalitis is a devastating disease, but unfortunately, worldwide, the causative virus in many cases is unknown. Therefore, it is important to identify viruses that could be responsible for cases of human encephalitis. Here, using metagenomic sequencing of CSF, we identified a gemykibivirus in a male child from Nepal with acute encephalitis syndrome (AES). We subsequently detected gemykibivirus DNA in CSF or serum of 12 more encephalitis patients by real-time PCR. The virus genomes we identified are highly similar to gemykibiviruses previously detected in CSF of three encephalitis patients from Sri Lanka. These results raise the possibility that gemykibivirus could be an underrecognized human pathogen., Competing Interests: The authors declare no conflict of interest.

Background: The 4 serotypes of dengue virus (DENV1-4) can each cause potentially deadly dengue disease, and are spreading globally from tropical and subtropical areas to more temperate ones. Nepal provides a microcosm of this global phenomenon, having met each of these grim benchmarks. To better understand DENV transmission dynamics and spread into new areas, we chose to study dengue in Nepal and, in so doing, to build the onsite infrastructure needed to manage future, larger studies., Methods and Results: During the 2022 dengue season, we enrolled 384 patients presenting at a hospital in Kathmandu with dengue-like symptoms; 79% of the study participants had active or recent DENV infection (NS1 antigen and IgM). To identify circulating serotypes, we screened serum from 50 of the NS1 + participants by RT-PCR and identified DENV1, 2, and 3 - with DENV1 and 3 codominant. We also performed whole-genome sequencing of DENV, for the first time in Nepal, using our new on-site capacity. Sequencing analysis demonstrated the DENV1 and 3 genomes clustered with sequences reported from India in 2019, and the DENV2 genome clustered with a sequence reported from China in 2018., Conclusion: These findings highlight DENV's geographic expansion from neighboring countries, identify China and India as the likely origin of the 2022 DENV cases in Nepal, and demonstrate the feasibility of building onsite capacity for more rapid genomic surveillance of circulating DENV. These ongoing efforts promise to protect populations in Nepal and beyond by informing the development and deployment of DENV drugs and vaccines in real time.

The clinical features of COVID-19 are vary widely, ranging from asymptomatic states or mild upper respiratory tract infections to severe pneumonia. Previous studies have shown that 20.0% of COVID-19 patients are hospitalized, out of which 10.0-20.0% are admitted to the Intensive Care Unit. The present study aims to assess predictors associated with COVID-19 leading to Intensive Care Unit admission among reverse transcriptase- polymerase chain reaction (RT-PCR) positive patients in Sukraraj Tropical and infectious disease hospital, Nepal. A case-control study was conducted from June 2022 to July 2022 among patients admitted to Sukraraj Tropical and Infectious Disease Hospital. A hospital-based age (± 2 years) and sex-matched case-control study design were adopted in which ICU admitted (case group, n = 33) and general ward admitted (control group, n = 66) were included. Data were collected using a structured questionnaire comprising of socio-demographic, clinical, and preventive predictors. Data were analyzed using the Statistical Package for Social Science version 11.5. The Chi-square test and conditional logistic regression to determine the predictors associated with ICU admission. High blood pressure, high C-reactive protein and poor application of preventive practices were found to be the predictors of ICU admission. Conditional logistics regression analyses revealed that independent risk factors associated with ICU admission were elevated blood pressure (AOR = 2.22; 95% CI 1.05-4.71, p = 0.015) and abnormal C-Reactive Protein (AOR = 2.92; 95% CI 1.24-6.84, p = 0.012) at the time of hospital admission were more likely to get admitted to ICU. Likewise, patients with poor preventive practice (AOR = 3.34; 95% CI 1.19-9.31, p = 0.02) more likely to get admitted to ICU than patient with good preventive practices.These research findings hold potential significance for facilitating early triage and risk assessment in COVID-19 patients., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Aryal et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

In Nepal, over 1 million individuals have tested positive for SARS-CoV-2. We sought to describe the frequency of nonrecovery from this infection at 6 months and associated symptoms. We conducted a retrospective cohort study of 6142 women who had positive and negative PCR tests for this infection 6 months previously at 3 institutions in Kathmandu. In telephone interviews women provided information on 22 symptoms and their intensities, health status and history, and functional status. Of 3732 women who had tested PCR positive, 630 (16.9%) reported that they were unrecovered. These 630 unrecovered women were distinguished statistically from the 3102 recovered women by more frequent histories of allergies, rheumatoid disease, BCG immunization, Covid vaccination, strep throat and recent URIs, and both weight gain and weight losses of more than 5 kg in the 6 months following testing, and stressful events in the preceding year. Fatigue, pain, difficulty remembering, shortness of breath, heat and cold intolerance and unrefreshing sleep were reported in 41.9% to 10.5% of these 630 unrecovered women. Six months after confirmed SARS-CoV-2 infection 16.9% of Nepali women have long-COVID manifested as an immune, metabolic, and hormonal systems disruptive and dysfunction syndrome., Competing Interests: The senior author, Dr. Richard Love, provided financial support for the data collection in this report. This does not alter our adherence to PLOS ONE policies on sharing data and materials., (Copyright: © 2024 Shrestha et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Nepal is an endemic country for dengue infection with rolling of every 3 year's clear cyclic outbreaks with exponential growth since 2019 outbreak and the virus gearing towards the non-foci temperate hill regions. However, the information regarding circulating serotype and genotype is not frequent. This research discusses on the clinical features, diagnosis, epidemiology, circulating serotype and genotype among 61 dengue suspected cases from different hospitals of Nepal during the window period 2017-2018 between the two outbreaks of 2016 and 2019. E-gene sequences from PCR positive samples were subjected to phylogenetic analysis under time to most recent common ancestor tree using Markov Chain Monte Carlo (MCMC) and BEAST v2.5.1. Both evolution and genotypes were determined based on the phylogenetic tree. Serotyping by Real-time PCR and Nested PCR showed the co-circulation of all the 3 serotypes of dengue in the year 2017 and only DENV-2 in 2018. Genotype V for DENV-1 and Cosmopolitan Genotype IVa for DENV-2 were detected. The detected Genotype V of DENV-1 in Terai was found close to Indian genotype while Cosmopolitan IVa of DENV-2 found spreading to geographically safe hilly region (now gripped to 9 districts) was close to South-East Asia. The genetic drift of DENV-2 is probably due to climate change and rapid viral evolution which could be a representative model for high altitude shift of the infection. Further, the increased primary infection indicates dengue venturing to new populations. Platelets count together with Aspartate transaminase and Aalanine transaminase could serve as important clinical markers to support clinical diagnosis. The study will support future dengue virology and epidemiology in Nepal., (© 2023. The Author(s).)

Like the world over, Nepal was also hard hit by the second wave of COVID-19. We audited the clinical care provided to COVID-19 patients admitted from April to June 2021 in a tertiary care hospital of Nepal. This was a cohort study using routinely collected hospital data. There were 620 patients, and most (458, 74%) had severe illness. The majority (600, 97%) of the patients were eligible for admission as per national guidelines. Laboratory tests helping to predict the outcome of COVID-19, such as D-dimer and C-reactive protein, were missing in about 25% of patients. Nearly all (>95%) patients with severe disease received corticosteroids, anticoagulants and oxygen. The use of remdesivir was low (22%). About 70% of the patients received antibiotics. Hospital exit outcomes of most (>95%) patients with mild and moderate illness were favorable (alive and discharged). Among patients with severe illness, about 25% died and 4% were critically ill, needing further referral. This is the first study from Nepal to audit and document COVID-19 clinical care provision in a tertiary care hospital, thus filling the evidence gap in this area from resource-limited settings. Adherence to admission guidelines was excellent. Laboratory testing, access to essential drugs and data management needs to be improved.

Introduction: The COVID-19 pandemic has affected the health systems in many ways. It has put unprecedented strain on health systems worldwide and exposed gaps in public health infrastructure. A health system comprises all institutions and resources working towards improving and maintaining health. Among the different aspects of health system strengthening, a patient's experiences and expectations play a crucial role in determining how well the health facilities function. This study aims to explore health system strengthening's implications based on experiences and feedback provided by COVID-19 patients admitted to a government tropical and infectious disease hospital in Nepal., Methods: In this qualitative study, we collected the voluntary handwritten feedback by the admitted COVID-19 patients to document the feedback and experiences from a book, maintained by the hospital. We performed thematic content analysis using the World Health Organization's six building blocks of health system as a theoretical framework which included service delivery, health workforce, information, leadership and governance, financing, and access to medicines., Results: Most patients in this study had positive experiences on service delivery and health workforce. Some also highlighted the gaps in infrastructure, cleanliness, and hygiene. Many suggested positive experiences on other dimensions of the health system such as financing, governance and leadership, and access to medicines reflected upon by the patients' thankfulness to the hospital and the government for the treatment they received. The responses also reflected the inter-connectedness between the different building blocks of health system., Conclusion: This study approached a unique way to strengthen the health system by exploring patients' feedback, which suggested an overall positive impression on most building blocks of health system. However, it also highlighted certain gaps in infrastructure, cleanliness, and hygiene. It reinforces the hospital management and government's role to continue its efforts to strengthen the health system., Competing Interests: The authors have declared that no competing interests exist.

Scrub typhus is caused by Orientia tsutsugamushi , transmitted through bites of infected chiggers (larval mites). During the coronavirus disease 2019 (COVID-19) pandemic, reports of co-infections with endemic pathogens are increasing around the world. Disease with similar clinical presentation may mask other disease diagnosis and increase the morbidity and mortality of the patients. We report co-infection between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and O. tsutsugamushi in a patient in Nepal presenting with fever, headache, retro-orbital pain, generalized body ache, and knee joints pain with a history of dry cough and dyspnea at night. Since scrub typhus is prevalent and considerate as one of the public health consents in Asian countries and the possible overlapping clinical manifestation with other infections including COVID-19, a further investigation required to determine the burden of SARS-CoV-2 and O. tsutsugamushi co-infection in scrub typhus-endemic countries in Asia., Competing Interests: Authors declare no conflict of interest., (© 2021 The Author(s).)

Coronavirus Disease 2019 (COVID-19) has challenged the health system worldwide, including the low and middle income countries like Nepal. In view of the rising number of infections and prediction of multiple waves of this disease, mortalities due to COVID-19 need to be critically analyzed so that every possible effort could be made to prevent COVID-19 related mortalities in future. Main aim of this research was to study about the mortalities due to COVID-19 at a tertiary level hospital, in Nepal. This was a retrospective, observational study that included all inpatients from Sukraraj Tropical and Infectious Disease Hospital, who were reverse transcriptase polymerase chain reaction positive for SARS-COV-2 and died during hospital stay from January 2020 till January 2021. Medical records of the patients were evaluated. Out of 860 total admissions in a year, there were 50 mortalities in the study center. Out of 50 mortalities, majority were males (76%) with male to female ratio of 3.17:1. Most were above 65 years of age (72%) and had two or more comorbidities (64%). The most common comorbidities among the patients who had died during hospital stay were hypertension (58%) followed by diabetes mellitus (50%) and chronic obstructive airway disease (24%). The median duration from the symptom onset to death was 18 days, ranged from the minimum of 2 days till maximum of 39 days. D-dimer was found to be >1 mg/L in 58% cases and ferritin was >500 ng/ml in 42% patients at presentation. A total of 42% patients had thrombocytopenia, 80% patients had lymphocytopenia and 60% had Neutrophil to Lymphocyte ratio >11.75 with the mean NLR of 18.38. Of total mortalities, 16% patients also showed microbiological evidence of secondary infection; Male gender, age more than 65 years, multiple comorbidities with lymphocytopenia, elevated Neutrophil lymphocyte ratio and elevated inflammatory markers were risk factors found in majority of mortalities in our study. These findings could be utilized for early triage and risk assessment in COVID-19 patients so that aggressive treatment strategies could be employed at the earliest to reduce mortalities due to COVID-19 in future.

The long-term effects of COVID-19 among survivors is a matter of concern. This research aimed to study persistent symptoms in post-COVID-19 patients attending a follow-up clinic at a tertiary care hospital in Nepal. All patients, presenting to the outpatient clinic during the study duration of six weeks, with history of positive reverse transcriptase- polymerase chain reaction for severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) at least two weeks prior to presentation, were included. The duration of follow-up ranged from 15 till 150 days with the mean duration of 28 days after diagnosis of COVID-19. Of 118 patients, 43 (36.4%) had a history of mild COVID-19, 15 (12.8%) had moderate, and 60 (50.8%) had severe. At the time of presentation, 97 (82.2%) patients reported that they had at least one persistent/new symptom beyond two weeks from the diagnosis of COVID-19. Dyspnea, fatigue, chest heaviness, and cough were the commonest persistent complaints in 48 (40.7%), 39 (33.1%), 33 (28%), and 32 (27.1%) patients, respectively. The findings in our study highlight the need for extended monitoring of post-COVID-19 patients following discharge, in order to understand and mitigate long-term implications of the disease.

A case of organophosphate (OP) poisoning who recovered after requiring almost 1000 mg of atropine, 10 gm of PAM and ventilatory support for 7 days is presented here. The overview of organophosphate poisoning and its management is given. With the approach adopted, the mortality reported in the general medicine unit in the central hospital in Nepal is 7.4%. The two important aspects of the management are vigilance of the atropine drip, especially at night, and other physical and psychological support care of the patients.