Sewage Analysis as a Tool for Environmental Surveillance of SARS-CoV-2: Experience from Delhi, India

Abstract

Background: The COVID-19 pandemic caused by SARS-CoV-2 has resulted in more than 150 thousand deaths in India. SARS-CoV-2 is known to be excreted in stool samples in the range of 102 to 108 gene copies per gram of faeces. Waste-water Based Epidemiology has been advocated by researchers all over the world as a method for environmental surveillance of COVID-19. Objectives: The present study was carried out to determine the presence of SARS-CoV-2, and to quantify it in sewage samples in Delhi, and to estimate the Sensitivity of WBE for COVID-19 Surveillance. Methods: A total of 49 waste water samples from seven different sites in Delhi were each concentrated by three different methods, Ultrafiltration, PEG precipitation and Two-phase separation method. RT-qPCR was done for N1, N2, and E gene of SARS-CoV-2. The minimum number of infected individuals required to yield a positive result was calculated. Results: Out of the 49 samples tested in triplicate, 35 (71.43%) were positive for at least one of the three primers for SARS-CoV-2 (N1, N2 or E) by Method A and 33(67.35%) by Method B. The average concentration calculated for Delhi, using data of the seven sites, was 1.25 x 104 g.c./L of sewage. Approximately 7.5 active cases per 1000 population are required to yield a positive result for Environmental Surveillance. Discussion: SARS-CoV-2 RNA could be successfully isolated from sewage samples in Delhi using Ultrafiltration and PEG precipitation for concentration. The practical limit of detection of the virus in waste water is low enough to make this a highly sensitive method for Environmental Surveillance of COVID-19. The detection of SARS-CoV-2 in sewage is a very useful tool with immense public health significance. It can provide an early warning signal of the presence of disease, and facilitate preparedness for the same.