ArticlePloS one2023
Rapid genomic surveillance of SARS-CoV-2 in a dense urban community of Kathmandu Valley using sewage samples.
Article in PloS one, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers, 1 of them a synthesis that pooled it.
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Who cites it
11 citing papers in PubMed, 1 synthesis or guideline pooled it, 20 citations in OpenAlex.
- Technological Barriers to Routine Genomic Surveillance for Vaccine Development Against SARS-CoV-2 in Africa: A Systematic Review.Influenza and other respiratory viruses · 2024Pooled it
- Human mobility and sewage data correlate with COVID-19 epidemic evolution in a 3-year surveillance of the metropolitan area of Bologna.BMC infectious diseases · 2025Article
- Dissemination of local sub-variants of SARS-CoV-2 detected by detailed mutation analysis in wastewater-based epidemiology.PloS one · 2025Article
- Application of Skimmed-Milk Flocculation Method for Wastewater Surveillance of COVID-19 in Kathmandu, Nepal.Pathogens (Basel, Switzerland) · 2024Article
- Elucidating the role of environmental management of forests, air quality, solid waste and wastewater on the dissemination of SARS-CoV-2.Hygiene and environmental health advances · 2022Review
- Review of concerned SARS-CoV-2 variants like Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529), as well as novel methods for reducing and inactivating SARS-CoV-2 mutants in wastewater treatment facilities.Journal of hazardous materials advances · 2022Review
- Rapid displacement of SARS-CoV-2 variant Delta by Omicron revealed by allele-specific PCR in wastewater.Water research · 2022Article
- Multifaceted Assessment of Wastewater-Based Epidemiology for SARS-CoV-2 in Selected Urban Communities in Davao City, Philippines: A Pilot Study.International journal of environmental research and public health · 2022Article
- Exploring the Genomic Landscape of Cancer Patient Cohorts with GenVisR.Current protocols · 2021Article
- Molecular Epidemiology of SARS-CoV-2 in Diverse Environmental Samples Globally.Microorganisms · 2021Article
- Spatial epidemiology and genetic diversity of SARS-CoV-2 and related coronaviruses in domestic and wild animals.PloS one · 2021Article
Corrections and comments
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Authors and funding
16 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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