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Environmental Surveillance for SARS-CoV-2 in Karachi: Correlating Sewage SARS-CoV-2 RNA Concentration and Reported Incidence of COVID-19 from a Large Urban District
22 Pages Posted: 9 Dec 2022
More...Abstract
Background: Wastewater-based surveillance has been used around the globe to track the presence and temporal patterns of the SARS-CoV-2 virus in communities. From the time of infection until 33 days later, the virus is shed in feces whereas a considerable percentage of COVID-19 cases remain are asymptomatic and are not included in clinical estimates. Therefore, viral RNA particle detection in wastewater samples can indicate the beginning of an outbreak within a catchment area well in advance of clinical surveillance. We describe the feasibility of using a sewage network to monitor the trend of SARS-CoV-2 and demonstrate the use of genomic sequencing to describe the variant abundance of the virus in an urban district in Karachi, Pakistan.
Methodology: We identified 4 sites draining into the Lyari River, the main open sewer in District East, Karachi, for collection of raw sewage samples. We used Bag Mediated Filtration System (BMFS) to collect early morning samples twice weekly from each site between June 10, 2021 and January 17, 2022. Secondary concentration of filtered samples was achieved by ultracentrifugation and skim milk flocculation in a BSL-2 laboratory. We tested samples with polymerase chain reaction test (PCR) using Qiagen ProMega kits for N1 & N2 genes. We used a distributed lag negative binomial regression model within a hierarchical Bayesian framework to describe the relationship between wastewater RNA concentration and COVID-19 cases from the catchment area. Genomic sequencing was performed using Illumina iSeq100.
Results: Using the bag-mediated filtration system (BMFS), we collected 151 raw sewage samples. In total, 123 (81.5%) sewage samples tested positive for the N1, N2, or E gene using reverse transcription polymerase chain reaction (RT-PCR).The limit of detection (LOD) for the positive samples was 6.67 gene copies/liter (gc/L). The average sewage RNA concentrations at each lag (1-14 days prior) were associated with current day’s cases/daily cases, with a peak association observed on lag day 10 (RR: 1.15; 95% CrI: 1.10 – 1.21). Next-generation genomic sequencing showed that the Delta variant dominated from June-September 2022, while, the Omicron variant was identified in November, one month before detection in clinical samples.
Conclusion: Wastewater-based surveillance provides valuable information for monitoring the temporal trend of SARS-CoV-2 in the community and together with next-generation genomic sequencing, can be used to complement clinical-based surveillance.
Funding Information: This study was funded by PATH (grant numbers: GAT.583722-01707644-CRT and 230 GIF.583820-01712491-CRT), the Bill & Melinda Gates Foundation (grant number INV-021602) and by the Global 231 Innovation Fund (PATH Covid-19 Environmental Surveillance, grant number 583820).
Declaration of Interests: The authors declare no competing interests.
Keywords: SARS-CoV-2 environmental surveillance, Karachi, Pakistan, SARS-CoV-2 genomic sequencing, SARS-CoV-2 variants, BMFS, grab method, SARS-CoV-2 sewage surveillance, wastewater-based epidemiology
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