Environmental surveillance for COVID-19 using SARS-CoV-2 RNA concentration in wastewater – a study in District East, Karachi, Pakistan.

Environmental surveillance for COVID-19 using SARS-CoV-2 RNA concentration in wastewater – a study in District East, Karachi, Pakistan.

Publication date: Jan 01, 2024

Wastewater-based surveillance is used to track the temporal patterns of the SARS-CoV-2 virus in communities. Viral RNA particle detection in wastewater samples can indicate an outbreak within a catchment area. We describe the feasibility of using a sewage network to monitor SARS-CoV-2 trend and use of genomic sequencing to describe the viral variant abundance in an urban district in Karachi, Pakistan. This was among the first studies from Pakistan to demonstrate the surveillance for SARS-CoV-2 from a semi-formal sewage system. Four sites draining into the Lyari River in District East, Karachi, were identified and included in the current study. Raw sewage samples were collected early morning twice weekly from each site between June 10, 2021 and January 17, 2022, using Bag Mediated Filtration System (BMFS). Secondary concentration of filtered samples was achieved by ultracentrifugation and skim milk flocculation. SARS-CoV-2 RNA concentrations in the samples were estimated using PCR (Qiagen ProMega kits for N1 & N2 genes). A distributed-lag negative binomial regression model within a hierarchical Bayesian framework was used to describe the relationship between wastewater RNA concentration and COVID-19 cases from the catchment area. Genomic sequencing was performed using Illumina iSeq100. Among the 151 raw sewage samples included in the study, 123 samples (81. 5%) tested positive for N1 or N2 genes. The average SARS-CoV-2 RNA concentrations in the sewage samples at each lag (1-14 days prior) were associated with the cases reported for the respective days, with a peak association observed on lag day 10 (RR: 1. 15; 95% Credible Interval: 1. 10-1. 21). Genomic sequencing showed that the delta variant dominated till September 2022, while the omicron variant was identified in November 2022. Wastewater-based surveillance, together with genomic sequencing provides valuable information for monitoring the community temporal trend of SARS-CoV-2. PATH, Bill & Melinda Gates Foundation, and Global Innovation Fund.

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Concepts Keywords
January BMFS
June Grab method
Pakistan Karachi
Pcr Pakistan
Sewage SARS-CoV-2 environmental surveillance
SARS-CoV-2 genomic sequencing
SARS-CoV-2 sewage surveillance
SARS-CoV-2 variants
Wastewater-based epidemiology


Type Source Name
disease MESH COVID-19
disease IDO site
drug DRUGBANK Dexketoprofen
disease VO USA
disease MESH Infectious Diseases
disease VO organization
drug DRUGBANK Coenzyme M
disease IDO pathogen
disease MESH influenza
disease VO effective
disease MESH infection
disease VO population
drug DRUGBANK Trestolone
drug DRUGBANK Water
disease VO Viruses
disease VO company
disease IDO process
disease VO efficiency
disease VO gene

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