Genomic surveillance reveals early detection and transition of Delta to Omicron Lineages of SARS-CoV-2 Variants in wastewater treatment plants of Pune, India

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.