ABSTRACT
The COVID-19 pandemic has emphasized the urgency for rapid public health surveillance methods in early detection and monitoring of the transmission of infectious diseases. The wastewater-based epidemiology (WBE) has emerged as a promising tool to analyze and enumerate the prevalence of infectious pathogens in a population ahead of time. In the present study, real time quantitative polymerase chain reaction (RT-qPCR) and Illumina sequencing was performed to determine the SARS-CoV-2 load trend and dynamics of variants over a longitudinal scale in 442 wastewater (WW) samples collected from 10 sewage treatment plants (STPs) of Pune city, India, during November 2021 to April-2022. In total 426 distinct lineages representing 17 highly transmissible variants of SARS-CoV-2 were identified. The SARS-CoV-2 Omicron variant fragments were detected in WW samples prior to its detection in clinical cases. Moreover, highly contagious sub-lineages of Omicron, such as BA.2.12 (0.8-0.25%), BA.2.38 (0.8-1.0%), BA.2.75 (0.01-0.02%), BA.3 (0.09-6.3%), BA.4 (0.24-0.29%), and XBB (0.01-13.7%) fragments were significantly detected. The longitudinal analysis also suggested the presence of the BA.5 lineage in November 2021, which was not reported in the clinical settings throughout the duration of this study, indicative of silent variant persistence. Overall, the present study demonstrated the practicality of WBE in early detection of SARS CoV-2 variants, which could be useful in tracking future outbreaks of SARS-CoV-2. Such approaches could be implicated in the monitoring of the infectious agents before they appear in clinical cases.
Subject(s)
Communicable Diseases , COVID-19ABSTRACT
Although the presence of SARS-CoV-2 fragments in raw sewage water are not much concerning, since it is a new pathogen and its fate in the environment is poorly understood; therefore efforts are needed for their effective removal. In under-developed countries with poor sewersheds and sanitation practices, the raw sewage water might come in contact with rivers and other water bodies and is generally used by the population for various purposes including drinking water. Hence it is important to properly treat sewage water to reduce public health risks, if any. Our study evaluated various advanced oxidation processes (AOPs) for disinfection of SARS-CoV-2 from sewage water collected from the academic institutional residential campus. The present study is the first report showing hydrodynamic cavitation (HC) used to reduce the SARS-CoV-2 viral load from sewage water. Additionally, we have also evaluated hybrid techniques like HC/O3, HC/O3/H2O2, HC/H2O2, O3/UV, UV/H2O2, UV/H2O2/O3, and O3/H2O2 for the minimization of the SARS-CoV-2 viral load from sewage water. The sewage water treatment techniques were evaluated based on its viral concentration-reducing efficiency by comparing it with the same raw sewage water sample. However, ozone alone and its combination with other disinfecting techniques (like HC, UV, and H2O2) showed >95% SARS-CoV-2 specific RNA-reducing efficiency (also known as viral load). The AOPs treated sewage water was subjected to total nucleic acid isolation followed by RT-qPCR for viral load estimation. Interestingly, all sewage water treatment techniques used in this study significantly reduces both the SARS-CoV-2 viral load as well as PMMoV (faecal indicator) load.
ABSTRACT
Given a large number of SARS-CoV-2 infected individuals, clinical detection has proved challenging. The wastewater-based epidemiological paradigm would cover the clinically escaped asymptomatic individuals owing to the faecal shedding of the virus. We hypothesised using wastewater as a valuable resource for analysing SARS-CoV-2 mutations circulating in the wastewater of Pune region (Maharashtra; India), one of the most affected during the covid-19 pandemic. We conducted a case study in open wastewater drains from December 2020-March 2021 to assess the presence of SARS-CoV-2 nucleic acid and further detect mutations using ARTIC protocol of MinION sequencing. The analysis revealed 108 mutations across six samples categorised into 40 types of mutations. We report the occurrence of mutations associated with B.1.617 lineage in March-2021 samples, simultaneously also reported as a Variant of Concern (VoC) responsible for the rapid increase in infections. The study also revealed four mutations; S:N801, S:C480R, NSP14:C279F and NSP3:L550del not currently reported from wastewater or clinical data in India but reported in the world. Further, a novel mutation NSP13:G206F mapping to NSP13 region was observed from wastewater. Notably, S:P1140del mutation was observed in December 2020 samples while it was reported in February 2021 from clinical data, indicating the instrumentality of wastewater data in early detection. This is the first study in India to conclude that wastewater-based epidemiology to identify mutations associated with SARS-CoV-2 virus from wastewater as an early warning indicator system.