Rapid genomic surveillance of SARS-CoV-2 in a dense urban community of Kathmandu Valley using sewage samples

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.

High‐resolution phylogeographical surveillance of Hantaan orthohantavirus using rapid amplicon‐based Flongle sequencing, Republic of Korea

“…The Oxford nanopore technologies enable the field diagnosis of infectious diseases via real‐time sequencing of viral genomes on a portable laptop, making it an appropriate device to be applied in POCT when we are faced with the epidemic of emerging viruses 15,40 . Recently, the Oxford Nanopore Flongle flow cell, a cost‐efficient single‐use chip (about $90 per chip), was developed and applied to rapid genome surveillance of severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) 41 . In this study, we established a rapid (within 3 h) nanopore‐based one‐step diagnostic assay using the single‐use Flongle chip for sensitive detection of HTNV.…”

Application of Skimmed-Milk Flocculation Method for Wastewater Surveillance of COVID-19 in Kathmandu, Nepal

“…Our correlation result also cautions against predicting future COVID-19 waves and the estimation of the number of COVID-19 cases based on wastewater concentration in settings with lower sewer coverage by WWTPs. Napit et al, 2023, conducted WS of SARS-CoV-2 in the same study area by collecting wastewater from sewers because of the possible underrepresentation of citywide wastewater by wastewater samples collected from the WWTP only [15]. It is generally recommended to downscale WS to a smaller area by sampling sewer lines corresponding to the area of interest to improve the accuracy of WS in LMICs where coverage of WWTPs is inadequate [16].…”