Campus Sewage Water Surveillance based dynamics and infection trends of SARS-CoV-2 variants during third wave of COVID-19 in Pune, India

The wastewater-based epidemiology (WBE) of SARS-CoV-2 is a quick and cost-effective method of tracking virus transmission. However, few studies reported on campus or in academic or residential settings worldwide. In this study, we demonstrated the WBE approach to detect, monitor, and evaluate genomic variants of SARS-CoV-2 fragments in a sewage treatment plant (STP) located on the campus of CSIR National Chemical Laboratory, Pune, India. Herein we describe the early warning capability of WBE, with viral load rise in campus sewage water up to 14 days before its clinical detection. This was supported further by a significant correlation between SARS-CoV-2 RNA concentration and clinically reported COVID-19 cases on campus. Additionally, we comprehended the probable targets missed by the quantitative qRT-PCR using amplicon-based sequencing due to low viral load. The analysis revealed the presence of signature mutations of the Omicron (S:N679K, S:N764K, S:D796Y, N:P13L, ORF1a:T3255I, ORF1a:K856R, ORF1a:P3395H, and N:S413R) before the lineage was first detected globally. Further, we used Lineage decomposition (LCS) tool to detect the Variant of Concern (VOC)/Variant of Interest (VOI) signals upto a month earlier in sewage water samples. The analysis also indicated the transition of lineage from Delta to Omicron in late Decemeber,2021. This is the first study in India highlighting the use of on-campus STP to evaluate the local spread of SARS-CoV-2, which could aid in preventing COVID-19 in academic institutes/universities. This study proves the usefulness of WBE as an early warning system for detecting, tracking and tracing VOCs using the sequencing approach. The current study could aid in taking critical decisions to tackle the pandemic scenario on campus. Highlights ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work is funded by a grant from Rockefeller Foundation, USA (Project code GAP 332926). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes