Wastewater surveillance of SARS-CoV-2 and influenza in preK-12 schools shows school, community, and citywide infections

Wolken, Madeline; Sun, Thomas; McCall, Camille; Schneider, Rebecca; Caton, Kelsey; Hundley, Courtney; Hopkins, Loren; Ensor, Katherine B.; Domakonda, Kaavya; Kalvapalle, Prashant; Persse, David; Williams, Stephen L.; Stadler, Lauren B.

doi:10.1016/j.watres.2023.119648

Cited by 35 publications

(32 citation statements)

References 50 publications

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“…Many human viruses are present in municipal wastewater, and wastewater measurements have been widely used for tracking viruses that cause human diseases such as polioviruses, SARS-CoV-2, influenza viruses, respiratory syncytial virus (RSV), human norovirus, Mpox (monkeypox), and other enteric and nonenteric viruses. − Beyond wastewater-based epidemiology (WBE) applications, wastewater virus measurements are also critical for determining the extent of advanced water treatment that is necessary in water reuse applications to achieve acceptable levels of risk in the finished drinking water. − Quantifying viruses in wastewater most frequently involves molecular-based methods (i.e., quantitative PCR methods) due to the limitations and complexities of culture-based methods. PCR-based quantification typically targets small portions of the viral genome, and therefore, the resulting concentrations are likely higher than infectious virus particles.…”

Section: Introductionmentioning

confidence: 99%

The Protective Effect of Virus Capsids on RNA and DNA Virus Genomes in Wastewater

Harrison,

Snead,

Kilts

et al. 2023

Environ. Sci. Technol.

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Virus concentrations measured in municipal wastewater help inform both the water treatment necessary to protect human health and wastewater-based epidemiology. Wastewater measurements are typically PCR-based, and interpreting gene copy concentrations requires an understanding of the form and stability of the nucleic acids. Here, we study the persistence of model virus genomes in wastewater, the protective effects provided by the virus capsids, and the relative decay rates of the genome and infectious viruses. In benchtop batch experiments in wastewater influent at 25 °C, extraviral (+)ssRNA and dsDNA amplicons degraded by 90% within 15−19 min and 1.6−1.9 h, respectively. When encapsidated, the T 90 for MS2 (+)ssRNA increased by 424× and the T 90 for T4 dsDNA increased by 52×. The (+)ssRNA decay rates were similar for a range of amplicon sizes. For our model phages MS2 and T4, the nucleic acid signal in untreated wastewater disappeared shortly after the viruses lost infectivity. Combined, these results suggest that most viral genome copies measured in wastewater are encapsidated, that measured concentrations are independent of assay amplicon sizes, and that the virus genome decay rates of nonenveloped (i.e., naked) viruses are similar to inactivation rates. These findings are valuable for the interpretation of wastewater virus measurements.

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Section: Introductionmentioning

confidence: 99%

The Protective Effect of Virus Capsids on RNA and DNA Virus Genomes in Wastewater

Harrison,

Snead,

Kilts

et al. 2023

Environ. Sci. Technol.

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show abstract

“…data available for FL and TX for wastewater but not available in FluSurv-NET). The wastewater data could also be used at more localized scales to identify peak events, as has been illustrated previously at the building 11 , subsewershed 9 , and sewershed 13 levels.…”

Section: Discussionmentioning

confidence: 97%

United States influenza 2022-2023 season characteristics as inferred from wastewater solids, influenza hospitalization and syndromic data

Schoen,

Bidwell,

Wolfe

et al. 2023

Preprint

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Influenza A virus (IAV) causes significant morbidity and mortality in the United States and has pandemic potential. Identifying IAV epidemic patterns is essential to inform the timing of vaccines and non-pharmaceutical interventions. In a prospective, longitudinal study design, we measured IAV RNA in wastewater settled solids at 163 wastewater treatment plants across 33 states to characterize the 2022-2023 influenza season at the state, health and human services (HHS) regional, and national scales. Influenza season onset, offset, duration, peak, and intensity using IAV RNA in wastewater were compared with those determined using laboratory-confirmed influenza hospitalization rates and outpatient visits for influenza-like illness (ILI). The onset for HHS regions as determined by IAV RNA in wastewater roughly corresponded with those determined using ILI when the annual geometric mean of IAV RNA concentration was used as baseline (i.e., the threshold that triggers onset), although offsets between the two differed. IAV RNA in wastewater provided early warning of onset, compared to the ILI estimate, when the baseline was set at twice the limit of IAV RNA detection in wastewater. Peak when determined by IAV RNA in wastewater generally preceded peak determined by IAV hospitalization rate by two weeks or less. Wastewater settled solids data is an IAV-specific indicator that can be used to augment clinical surveillance for seasonal influenza epidemic timing and intensity.

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“…On a few occasions, we identified strains from distinct patients that were closely related ( i.e., < 30 SNPs) consistent with hospital acquisition, but most strains were genetically diverse suggesting a community source. Given the recent success of wastewater surveillance in identifying SARS-CoV-2 and influenza transmission dynamics (40, 41), we envision that a similar approach could be used to improve understanding of how community prevalence of ESC-R pathogens impacts subsequent infections.…”

Section: Discussionmentioning

confidence: 99%

Temporal Dynamics of Genetically Heterogeneous Extended-Spectrum Cephalosporin ResistantEscherichia coliBloodstream Infections

Shropshire

Strope

Anand

et al. 2023

Preprint

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Extended-spectrum cephalosporin resistant (ESC-R) Escherichia coli (ESC-R-Ec) is an urgent public health threat with clonal complex (CC) 131, phylogroup B2 strains being particularly concerning as the dominant cause of ESC-R-Ec infections. To address the paucity of recent ESC-R-Ec molecular epidemiology data in the United States (US), we used whole genome sequencing (WGS) to fully characterize a large cohort of invasive ESC-R-Ec at a tertiary care cancer center in Houston, Texas collected from 2016-2020. During the study timeframe, there were 1154 index E. coli bloodstream infections (BSIs) of which 389 (33.7%) were ESC-R. Using time series analyses, we identified a temporal dynamic of ESC-R E. coli BSIs (Ec-BSIs), distinct from ESC-susceptible Ec-BSIs, with cases peaking in the last 6 months of the calendar year. WGS of 297 ESC-R Ec-BSI strains revealed that while CC131 strains accounted for ~45% of total infections, the proportion of CC131 strains remained stable across the time-period, and infection peaks were driven by genetically diverse, non-CC131 isolates. BlaCTX-M variants accounted for most beta-lactamases conferring the ESC-R phenotype (89%; 220/248 index ESC-R Ec-BSIs), and amplification of blaCTX-M genes was widely detected in ESC-R Ec-BSI strains, particularly in carbapenem non-susceptible strains and in strains causing recurrent BSIs. BlaCTX-M-55 was significantly enriched within phylogroup A strains, and we identified blaCTX-M-55 plasmid-to-chromosome transmission occurring across non-B2 strains. Our data provide important information regarding the current molecular epidemiology of invasive ESC-R E. coli and provide novel insights into the genetic basis of observed temporal variability for these clinically important pathogens.

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Wastewater surveillance of SARS-CoV-2 and influenza in preK-12 schools shows school, community, and citywide infections

Cited by 35 publications

References 50 publications

The Protective Effect of Virus Capsids on RNA and DNA Virus Genomes in Wastewater

The Protective Effect of Virus Capsids on RNA and DNA Virus Genomes in Wastewater

United States influenza 2022-2023 season characteristics as inferred from wastewater solids, influenza hospitalization and syndromic data

Temporal Dynamics of Genetically Heterogeneous Extended-Spectrum Cephalosporin ResistantEscherichia coliBloodstream Infections

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