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Understanding disease burden and transmission dynamics in resource-limited, low-income countries like Nepal are often challenging due to inadequate surveillance systems. These issues are exacerbated by limited access to diagnostic and research facilities throughout the country. Nepal has one of the highest COVID-19 case rates (915 cases per 100,000 people) in South Asia, with densely-populated Kathmandu experiencing the highest number of cases. Swiftly identifying case clusters (hotspots) and introducing effective intervention programs is crucial to mounting an effective containment strategy. The rapid identification of circulating SARS-CoV-2 variants can also provide important information on viral evolution and epidemiology. Genomic-based environmental surveillance can help in the early detection of outbreaks before clinical cases are recognized and identify viral micro-diversity that can be used for designing real-time risk-based interventions. This research aimed to develop a genomic-based environmental surveillance system by detecting and characterizing SARS-CoV-2 in sewage samples of Kathmandu using portable next-generation DNA sequencing devices. Out of 22 sites in the Kathmandu Valley from June to August 2020, sewage samples from 16 (80%) sites had detectable SARS-CoV-2. A heatmap was created to visualize the presence of SARS-CoV-2 infection in the community based on viral load intensity and corresponding geospatial data. Further, 47 mutations were observed in the SARS-CoV-2 genome. Some detected mutations (n = 9, 22%) were novel at the time of data analysis and yet to be reported in the global database, with one indicating a frameshift deletion in the spike gene. SNP analysis revealed possibility of assessing circulating major/minor variant diversity on environmental samples based on key mutations. Our study demonstrated the feasibility of rapidly obtaining vital information on community transmission and disease dynamics of SARS-CoV-2 using genomic-based environmental surveillance.

In Nepal, rapid urbanization and rural-to-urban migration especially due to internal civil conflict have catalyzed the development of temporary settlements, often along rivers on undeveloped land. This study conducted surveillance for viruses in small mammals and assessed potential risks for virus transmission to people in urban settlements along rivers in Kathmandu, Nepal. We collected samples from 411 small mammals (100 rodents and 311 shrews) at four riverside settlement sites and detected six viruses from four virus families including Thottapalayam virus; a strain of murine coronavirus; two new paramyxoviruses; and two new rhabdoviruses. Additionally, we conducted surveys of 264 residents to characterize animal-human contact. Forty-eight percent of individuals reported contact with wildlife, primarily with rodents and shrews (91%). Our findings confirm that rodents and shrews should be considered a health threat for residents of temporary settlements, and that assessment of disease transmission risk coupled with targeted surveillance for emerging pathogens could lead to improved disease control and health security for urban populations. Additionally, interventions focused on disease prevention should consider the unique urban ecology and social dynamics in temporary settlements, along with the importance of community engagement for identifying solutions that address specific multi-dimensional challenges that life on the urban river margins presents.

Abstract Background The true prevalence of HIV and other sexually transmitted diseases among street children in Nepal is virtually unknown while information on related behavioural risk factors in this population is non-existent. The risk of HIV infection among street children and adolescents may be especially high due to their marginalized social and economic conditions. This study was conducted to determine the prevalence of HIV infection among a sample of street children and youth of Kathmandu and to identify risk factors associated with HIV infection in this group. A sample of street children and youth was recruited based on the purposive sampling of ten streets in Kathmandu, Nepal, known to have a high density of street children and youth. A total of 251 street children (aged 11–16 years) and youth (aged 17–24 years) were enrolled, with informed consent, from November, 2008 through June, 2009. Most of the participants (95%) were male. Case status was determined by serological assessment of HIV status; data on risk factors were obtained using structured survey interviews. HIV prevalence and rates of a number of behavioural risk factors suspected to play a role in HIV transmission among street children and youth were determined, including unprotected sex, intravenous drug use, and other risky sex and substance use behaviours. Results Among the 251 children and youth, we found an overall HIV prevalence of 7.6%. As the sample size of females was small (n = 13) and the behavioural risk factors are likely to be quite different for boys and girls, we conducted separate analyses by gender. As our small sample of females is unlikely to be representative and lacks power for statistical testing, our report focuses on the results for the males surveyed.The strongest behavioural risk factor to emerge from this study was intravenous drug use; 30% of the male subjects were injecting drug users and 20% of those were HIV positive. Furthermore, frequency of drug injection was a highly significant predictor with a dose–response relationship; males reporting occasional injection drug use were nearly 9 times more likely to be HIV positive than never users, while weekly drug injectors had over 46 times the risk of non-users, controlling for exposure to group sex, the only other significant risk factor in the multivariate model. Conclusions This sample of street children and youth of Kathmandu has a nearly 20-fold higher prevalence of HIV infection than the general population of Nepal (0.39%). The children and youth engage in number of high risk behaviours, including intravenous drug use, putting them at significant risk of contracting HIV and other sexually transmitted infections.

Background: HIV is a major public health issue around the world, especially in developing countries. Although the overall prevalence of HIV in Nepal is relatively low, there are specific sub-populations where the prevalence is far higher than the national average. One of these sub-groups is male people who inject drugs (male PWIDs). In order to understand the reasons for the differences in prevalence, a series of socio-demographic, behavioural and knowledge-based risk factors need to be assessed. Methods: The study used a series of 7 cross-sectional survey datasets from Pokhara (Nepal), collected between 2003 and 2017 (N = 2235) to investigate trends in HIV prevalence among male PWIDs by socio-demographic and behavioural and knowledge-based risk factors. A series of logistic regression models were conducted to investigate the association between study factors and HIV. Results: HIV prevalence decreased from the levels seen in 2003 (22.0%) and 2005 (21.7%), with the lowest prevalence recorded in 2015 (2.6%), however prevalence has increased in the most recent period (4.9%). A lower risk of HIV was associated with younger age (<=24 years compared to > 24 years, OR = 0.17, 95% CI = 0.10-0.31), being married (OR = 1.91, 95% CI = 1.25-3.02) and shorter duration of drug use (<=4 years compared to > 4 years, OR = 0.16, 95% CI = 0.09-0.29). A higher risk of HIV was associated with low (compared to secondary or higher) education level (OR = 2.76, 95% CI = 1.75-4.36), a lack of addiction treatment (OR = 2.59, 95% CI = 1.64-4.08), and recent use of unsterilized injection equipment (OR = 2.22, 95% CI = 1.20-4.11). Conclusion: The prevalence of HIV in male PWIDs in Pokhara has been variable, but overall has reduced in recent years to 2.6% before increasing in 2017 to 4.9%. The main determinants which increase the risk of HIV among male PWIDs in Pokhara are low education level, a lack of treatment for drug addiction and the recent use of unsterilised equipment. Each of these indicate the need to improve addiction treatment and education programs for intravenous drug use to aid this key population in avoiding risk-taking behaviours. [ABSTRACT FROM AUTHOR]

A disproportionate number of street children use and inject drugs and engage in survival sex as coping mechanisms. This study aimed to determine the prevalence of drug use, injecting drugs, survival sex, and condom use and determinants associated with these behaviors among street children. Cross-sectional surveys were conducted in 2016 with an aim to sample 350 street children and youths in Kathmandu Valley, Nepal. Information about sociodemographic characteristics, injecting drugs, sexual risk behaviors, and biological specimens for HIV testing were obtained. The logistic regression model was used to identify the determinants associated with drug use, injecting drugs, survival sex, and condom use during last sex. Variables that were significantly associated with being a current drug user (versus never) in the presence of other variables included being a rag picker (adjusted odds ratio [AOR] = 3.2; 95% confidence interval [95% CI] = 1.73-5.9), history of imprisonment (AOR = 2.21; 95% CI = 1.21-4.04), alcohol consumption (AOR = 2.66; 95% CI = 1.46-4.84), and solvent sniffing (AOR = 5.12; 95% CI = 2.74-9.59). Variables that were significantly predictive of injecting drugs (versus never) in the presence of other variables include being 17 years old (AOR = 3.42; 95% CI = 1.11-10.55) and being a rag picker (AOR = 3.5; 95% CI = 1.25-9.75). Variables that were significantly associated with having survival sex (versus never) in the presence of other variables include being 17 years old (AOR = 3.58; 95% CI = 1.31-9.81) and having forced sex (AOR = 9.62; 95% CI = 3.21-28.8). Drug use and survival sex are major coping mechanisms among street children in Kathmandu Valley and are associated with many risk behaviors. Targeted programs should be implemented to meet their special needs. [ABSTRACT FROM AUTHOR]