Rapid genomic surveillance of SARS-CoV-2 in a dense urban community using environmental (sewage) samples

Abstract

Understanding disease burden and transmission dynamics in resource-limited, developing countries like Nepal is often challenging due to a lack of adequate 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 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 20 selected sites in the Kathmandu Valley, sewage samples from 16 (80%) sites had detectable SARS-CoV-2. A heat-map was created to visualize transmission activity in the community based on viral load intensity and corresponding geospatial data. Further, 41 mutations were observed in the SARS-CoV-2 genome. Some detected mutations (n=9, 2%) were novel and yet to be reported in the global database, with one indicating a frameshift deletion in the spike gene. We also observed more transition than transversion on detected mutations, indicating rapid viral evolution in the host. Our study has demonstrated the feasibility of rapidly obtaining vital information on community transmission and disease dynamics of SARS-CoV-2 using genomic-based environmental surveillance.

Quantitative SARS-CoV-2 tracking of variants Delta, Delta plus, Kappa and Beta in wastewater by allele-specific RT-qPCR

“…A companion to clinical surveillance is wastewater-based surveillance, which has been shown to be effective at capturing temporal trends in viral circulation during this COVID-19 pandemic (Hassard et al, 2021;Thompson et al, 2020;Wu et al, 2020a). Current mainstream methods for variant tracking in wastewater rely on enriching and sequencing of the environmental SARS-CoV-2 genome (Napit et al, 2021, Crits-Christoph et al, 2021Fontenele et al, 2021). This method, constrained by the same bottlenecks of cost and infrastructure requirement as clinical sequencing, is further hampered by challenges in detection of low-frequency variants and is poorly quantitative due to the lack of robust modelling to quantify variant titers (Fuqua et al, 2021;Van Poelvoorde et al, 2021) .…”

Molecular Epidemiology of SARS-CoV-2 in Diverse Environmental Samples Globally

“…The most common amino acid substitutions were D614G in the S glycoprotein of environmental strains that are commonly circulating among the clinical human samples [ 50 , 51 ]. This mutation increases the transmissibility and mortality rates [ 52 ].…”

Wastewater-Based Epidemiology and Whole-Genome Sequencing for Community-Level Surveillance of SARS-CoV-2 in Selected Urban Communities of Davao City, Philippines: A Pilot Study

“…In most cities, the sewage flow rate is greatest during the morning and the evening, and a 24-hour composite sampling can catch these peak flows with the most reliable mean viral levels in the wastewater (Michael-Kordatou et al, 2020). However, composite samples may also result in reduced viral titers compared to grab sampling (Michael-Kordatou et al, 2020, Nemudryi et al, 2020 PREPRINT) because of the dilution of viruses (Napit et al, 2021 PREPRINT). In addition, composite sampling is also logistically challenging, especially without expensive automated wastewater collectors.…”

“…In this study, grab samples were collected between 8 AM to 3 PM, depending on the site’s distance from the laboratory and the changing of tides (for sites near the Davao Gulf). For future studies, the collection of grab samples during peak hours of human toilet use (e.g., 7 AM to 9 AM) is an alternative method that can improve the chances of detecting fecally shed SARS-CoV-2, especially in low-incidence and low-resource areas (Napit et al, 2021 PREPRINT).…”

“…In Brazil (Prado et al, 2021) and Singapore (Wong et al, 2021), WBE data from samples from sewer pipes were used to determine where public health interventions should be intensified. Circulating variants and strains of SARS-CoV-2 were identified in wastewater using whole-genome sequencing (WGS), supporting the use of wastewater surveillance for tracing variant importations and circulation (Martin et al, 2020; Crits-Christoph et al, 2021; Napit et al,2021 PREPRINT).…”