Baseline Sequencing Surveillance of Public Clinical Testing, Hospitals, and Community Wastewater Reveals Rapid Emergence of SARS-CoV-2 Omicron Variant of Concern in Arizona, USA

Smith, Matthew F.; Holland, Steven C.; Lee, Mihyun B; Hu, James C; Pham, Nghia C; Sullins, Regan A; Holland, LaRinda A; Mu, Tianchen; Thomas, Alexis W; Fitch, Remington; Driver, Erin M.; Halden, Rolf U.; Villegas-Gold, Michelle; Sanders, Sheri; Krauss, Jennifer L.; Nordstrom, Lora; Mulrow, Mary; White, Michael; Murugan, Vel; Lim, Efrem S.

doi:10.1128/mbio.03101-22

Cited by 13 publications

(18 citation statements)

References 53 publications

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“…During our year-long 2022 surveillance study, SARS-CoV-2 case rates in Tempe strongly correlated with wastewater viral load ( Figure 4A and 4B , linear regression with Kendall’s rank correlation τ = 0.593). We compared the distribution of SARS-CoV-2 variants inferred from wastewater sequencing data to our ongoing baseline genomic surveillance efforts (13) in Tempe communities (n = 32,891 sequenced cases). The three major waves of Omicron BA.1, BA.2 and BA.5 in the population was correspondingly observed in wastewater lineage calls ( Figure 4C ).…”

Section: Resultsmentioning

confidence: 99%

“…PCR-based analysis of wastewater for SARS-CoV-2 (e.g., qRT-PCR, RT-dPCR) can supplement public health data by providing real-time data on population-level disease prevalence and has been shown to be less prone to sampling bias when compared to clinical surveillance of individuals (9). Furthermore, genomic sequencing of wastewater provided information about circulating SARS-CoV-2 variants by revealing cryptic lineages previously unobserved in clinical surveillance (10,11) and early warning of emerging SARS-CoV-2 variants of concern (12,13). This showcased the potential for wastewater surveillance in monitoring emergent pathogen threats (14)(15)(16).…”

Section: Introductionmentioning

confidence: 99%

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Seasonality of Respiratory, Enteric and Urinary Viruses Revealed by Wastewater Genomic Surveillance

Smith,

Maqsood,

Sullins

et al. 2024

Preprint

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Wastewater surveillance can reveal population-level infectious disease burden and emergent public health threats can be reliably assessed through wastewater surveillance. While molecular methods for wastewater monitoring of microorganisms have traditionally relied on PCR-based approaches, next-generation sequencing can provide deeper insights via genomic analyses of multiple diverse pathogens. We conducted a year-long sequencing surveillance of 1,408 composite wastewater samples collected from 12 neighborhood-level access points in the Greater Tempe area, Arizona, USA, and show that variation in wastewater viromes is driven by seasonal time and location. Wastewater virome temporal dynamics were influenced in a cyclical manner, with the most dissimilarity between samples 23 weeks apart (i.e., winter vs summer, spring vs fall). We identified diverse urinary and enteric viruses including polyomaviruses, astroviruses and noroviruses, and showed that their genotypes/subtypes shifted across season. We show that while wastewater data of certain respiratory viruses like SARS-CoV-2 strongly correlate with clinical case rates, laboratory-reported case incidences were discordant with surges of high viral load in wastewater for other viruses like human coronavirus 229E. These results demonstrate the utility of wastewater sequencing for informing decision making in public health.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Seasonality of Respiratory, Enteric and Urinary Viruses Revealed by Wastewater Genomic Surveillance

Smith,

Maqsood,

Sullins

et al. 2024

Preprint

Self Cite

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“…Since then, the recombinant XBB (Nextstrain clade 22F) has risen to global abundance, and convergent mutations have made it increasingly challenging to disentangle lineages. As we write, SARS-CoV-2 genome sequencing has been deployed in wastewater from across the globe (e.g., USA, Canada, Uruguay, Japan, Italy, India, Spain) to augment surveillance efforts during Gamma, Delta, and Omicron (BA.1 to XBB/BQ) waves 12,13,25,26,48 . The uptake of wastewater sequencing data to bring lineage-level information to WBS highlights the importance of benchmarking and developing standards.…”

Section: Discussionmentioning

confidence: 99%

“…A variety of computational tools have been developed recently to address the challenges of wastewater sequencing, with the common goal of inferring the presence and (in most cases) the relative abundances of various SARS-CoV-2 lineages present in wastewater. In this benchmark, we focus on SARS-CoV-2 whole-genome sequencing using short reads from tiled amplicons to identify specific viral lineages and their relative abundances 26 . This approach is currently more commonly used than long-read sequencing 27 .…”

Section: Introductionmentioning

confidence: 99%

Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data

Sutcliffe,

Kraemer,

Ellmen

et al. 2023

Preprint

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Wastewater-based surveillance (WBS) is an important epidemiological and public health tool for tracking pathogens across the scale of a building, neighbourhood, city, or region. WBS gained widespread adoption globally during the SARS-CoV-2 pandemic for estimating community infection levels by qPCR. Sequencing pathogen genes or genomes from wastewater adds information about pathogen genetic diversity which can be used to identify viral lineages (including variants of concern) that are circulating in a local population. Capturing the genetic diversity by WBS sequencing is not trivial, as wastewater samples often contain a diverse mixture of viral lineages with real mutations and sequencing errors, which must be deconvoluted computationally from short sequencing reads. In this study we assess nine different computational tools that have recently been developed to address this challenge. We simulated 100 wastewater sequence samples consisting of SARS-CoV-2 BA.1, BA.2, and Delta lineages, in various mixtures, as well as a Delta-Omicron recombinant and a synthetic “novel” lineage. Most tools performed well in identifying the true lineages present and estimating their relative abundances, and were generally robust to variation in sequencing depth and read length. While many tools identified lineages present down to 1% frequency, results were more reliable above a 5% threshold. The presence of an unknown synthetic lineage, which represents an unclassified SARS-CoV-2 lineage, increases the error in relative abundance estimates of other lineages, but the magnitude of this effect was small for most tools. The tools also varied in how they labelled novel synthetic lineages and recombinants. While our simulated dataset represents just one of many possible use cases for these methods, we hope it helps users understand potential sources of noise or bias in wastewater sequencing data and to appreciate the commonalities and differences across methods.

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“…Due to the improvement of molecular techniques to enrich genomes of interest and reduce assay inhibition, next generation sequencing across whole genomes from species present in wastewater at low-abundance is possible (Child et al, 2023). This enables improved public health monitoring of disease outbreaks and monitoring for immunologically relevant mutations of interest across whole genomes (Smith et al, 2023).…”

Section: Introductionmentioning

confidence: 99%

Human adenovirus outbreak at a university campus monitored by wastewater and clinical surveillance

Holland,

Smith,

Holland

et al. 2024

Preprint

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Areas of dense population congregation are prone to experience respiratory virus outbreaks. We monitored wastewater and clinic patients for the presence of respiratory viruses on a large, public university campus. Campus sewer systems were monitored in 16 locations for the presence of viruses using next generation sequencing over 22 weeks in 2023. During this period, we detected a surge in human adenovirus (HAdV) levels in wastewater. Hence, we initiated clinical surveillance at an on-campus clinic from patients presenting with acute respiratory infection. From whole genome sequencing of 123 throat and/or nasal swabs collected, we identified an outbreak of HAdV, specifically of HAdV-E4 and HAdV-B7 genotypes overlapping in time. The temporal dynamics and proportions of HAdV genotypes found in wastewater were corroborated in clinical infections. We tracked specific single nucleotide polymorphisms (SNPs) found in clinical virus sequences and showed that they arose in wastewater signals concordant with the time of clinical presentation, linking community transmission of HAdV to the outbreak. This study demonstrates how wastewater-based epidemiology can be integrated with surveillance at ambulatory healthcare settings to monitor areas prone to respiratory virus outbreaks and provide public health guidance.

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Baseline Sequencing Surveillance of Public Clinical Testing, Hospitals, and Community Wastewater Reveals Rapid Emergence of SARS-CoV-2 Omicron Variant of Concern in Arizona, USA

Abstract: SARS-CoV-2 continues to evolve new variants throughout the pandemic. However, the temporal dynamics of how SARS-CoV-2 variants emerge to become the dominant circulating variant is not precisely known.

Cited by 13 publications

References 53 publications

Seasonality of Respiratory, Enteric and Urinary Viruses Revealed by Wastewater Genomic Surveillance

Seasonality of Respiratory, Enteric and Urinary Viruses Revealed by Wastewater Genomic Surveillance

Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data

Human adenovirus outbreak at a university campus monitored by wastewater and clinical surveillance

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