Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission

Abstract

As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing and/or sequencing capacity, which can also introduce biases1–3. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing4,5. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We developed and deployed improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detected emerging variants of concern up to 14 days earlier in wastewater samples, and identified multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission.

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

“…To address these issues, we developed QuaID: a computational pipeline for analyzing SARS-CoV-2 wastewater sequencing data and inferring presence of VoCs. We use empirical results on real Houston wastewater data and simulated data to validate the efficacy of our software, and compare it to Freyja 4 , another state-of-the-art tool for VoC detection. Our key goal is achieving sensitivity to newly emerging variants in scenarios where coverage breadth and depth can be uneven, and the VoC-associated genomes are present at low abundances.…”

“…Wastewater monitoring is an invaluable tool for SARS-CoV-2 surveillance [1][2][3][4][5][6][7][8] . Despite multiple recent successes in VoC monitoring and detection from wastewater sequencing data [9][10][11][12][13][14][15] , there are multiple challenges associated with the nature of the environmental data. Since wastewater represents a pooled sample of multiple hosts, it harbors a diversity of SARS-CoV-2 variants that are currently circulating in the population 1,2,10,13 , including potentially previously unreported genotypes 16 .…”

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

“…Clinical samples were sequenced from a selected hospital which is not representative of the Bangalore population. Karthikeyan et al 19 observed varying periods of VOC lineage detection relative to clinical genomic surveillance, which was attributed to different virus shedding characteristics across lineages 20 .…”

What poo tells us: wastewater surveillance comes of age amid covid, monkeypox, and polio

“…Based on a 295 day comparison between wastewater and clinical sequences at the University of California, San Diego, a large collaborative effort likewise detected emerging variants of concern in wastewater samples up to two weeks before their identification in clinical samples, along with “multiple instances of virus spread not captured by clinical genomic surveillance.”5…”