SARS-CoV-2 infection dynamics and genomic surveillance reveals early variant transmission in urban wastewater

Abstract

Environmental surveillance (ES) of a pathogen is crucial for understanding the community load of disease. As an early warning system, ES for SARS–CoV–2 has complemented routine diagnostic surveillance by capturing near real–time virus circulation at a population level. In this longitudinal study in 28 sewershed sites in Bangalore city, we quantified SARS–CoV–2 RNA to track infection dynamics and provide evidence of change in the relative abundance of emerging variants. We describe an early warning system using the exponentially weighted moving average control chart and demonstrate how SARS–CoV–2 RNA concentrations in wastewater correlated with clinically diagnosed new COVID–19 cases, with the trends appearing 8–14 days earlier in wastewater than in clinical data. This was further corroborated by showing that the estimated number of infections is strongly correlated with SARS–CoV–2 RNA copies detected in the wastewater. Using a deconvolution matrix, we detected emerging variants of concern up to two months earlier in wastewater samples. In addition, we found a huge diversity in variants detected in wastewater compared to clinical samples. Our study highlights that quantifying viral titres, correlating it with a known number of cases in the area, and combined with genomic surveillance helps in tracking VOCs over time and space, enabling timely and making informed policy decisions.

QuaID: Enabling Earlier Detection of Recently Emerged SARS-CoV-2 Variants of Concern in Wastewater

“…Wastewater monitoring of the SARS-CoV-2 variant emergence and spread offers unique benefits based on the early detection of the variant arrival prior to the clinical data 3,34,35,15,25 , and broad surveillance coverage of the population 20,34,36,37 . QuaID offers a highly sensitive pipeline for VoC detection using wastewater SARS-CoV-2 sequencing data.…”

“…Furthermore, variant detection and phasing is further complicated by uneven genome coverage 2,17,18 and environmental RNA degradation 5,19,20 which render phased assembly extremely difficult [21][22][23] . Despite these challenges, detection of VoCs in wastewater samples is important for monitoring the emergence and spread of variants and informing public health response 4,5,11,24,25 . Current approaches for VoC detection in wastewater samples typically require sufficient depth and breadth of coverage of the variant genomes 9,12 , and therefore depend on a large fraction of the sample representing the variant genotype 10 , hampering early detection.…”

Wastewater surveillance of open drains for mapping the trajectory and succession of SARS-CoV-2 lineages in 23 class-I cities of Maharashtra State (India) during June 2022 to May 2023

“…2022). This data can then be used for retrospective analysis to trace back the source communities (Lamba et. al., 2022), aiding in the early detection of COVID-19 infections up to several weeks before cases are clinically reported at a city-wide scale.…”