Evaluation of a Wastewater-Based Epidemiological Approach to Estimate the Prevalence of SARS-CoV-2 Infections and the Detection of Viral Variants in Disparate Oregon Communities at City and Neighborhood Scales,Environmental Health Perspectives

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Evaluation of a Wastewater-Based Epidemiological Approach to Estimate the Prevalence of SARS-CoV-2 Infections and the Detection of Viral Variants in Disparate Oregon Communities at City and Neighborhood Scales
Environmental Health Perspectives ( IF 10.1 ) Pub Date : 2022-6-29 , DOI: 10.1289/ehp10289
Blythe A Layton _{1,

2} , Devrim Kaya ₁ , Christine Kelly ₁ , Kenneth J Williamson ₂ , Dana Alegre ₃ , Silke M Bachhuber ₄ , Peter G Banwarth ₅ , Jeffrey W Bethel ₆ , Katherine Carter ₃ , Benjamin D Dalziel _{4,

7} , Mark Dasenko ₃ , Matthew Geniza ₃ , Andrea George _{1,

2} , Anne-Marie Girard ₃ , Roy Haggerty ₈ , Kathryn A Higley ₉ , Denise M Hynes _{3,

10,

11} , Jane Lubchenco ₄ , Katherine R McLaughlin ₁₂ , F Javier Nieto ₁₁ , Aslan Noakes ₈ , Matthew Peterson ₃ , Adriana D Piemonti ₂ , Justin L Sanders ₁₃ , Brett M Tyler _{3,

14} , Tyler S Radniecki ₁

Affiliation

School of Chemical, Biological, and Environmental Engineering, Oregon State University (OSU), Corvallis, Oregon, USA.
Department of Research and Innovation, Clean Water Services, Hillsboro, Oregon, USA.
Center for Quantitative Life Sciences, OSU, Corvallis, Oregon, USA.
Department of Integrative Biology, OSU, Corvallis, Oregon, USA.
Benton County Health Department, Corvallis, Oregon, USA.
School of Biological and Population Health Sciences, OSU, Corvallis, Oregon, USA.
Department of Mathematics, OSU, Corvallis, Oregon, USA.
College of Science, OSU, Corvallis, Oregon, USA.
School of Nuclear Science and Engineering, OSU, Corvallis, Oregon, USA.
U.S. Department of Veterans Affairs, Portland, Oregon, USA.
College of Public Health and Human Sciences, OSU, Corvallis, Oregon, USA.
Department of Statistics, OSU, Corvallis, Oregon, USA.
Carlson College of Veterinary Medicine, OSU, Corvallis, Oregon, USA.
Departmehnt of Botany and Plant Pathology, OSU, Corvallis, Oregon, USA.

Abstract

Background:

Positive correlations have been reported between wastewater SARS-CoV-2 concentrations and a community’s burden of infection, disease or both. However, previous studies mostly compared wastewater to clinical case counts or nonrepresentative convenience samples, limiting their quantitative potential.

Objectives:

This study examined whether wastewater SARS-CoV-2 concentrations could provide better estimations for SARS-CoV-2 community prevalence than reported cases of COVID-19. In addition, this study tested whether wastewater-based epidemiology methods could identify neighborhood-level COVID-19 hotspots and SARS-CoV-2 variants.

Methods:

Community SARS-CoV-2 prevalence was estimated from eight randomized door-to-door nasal swab sampling events in six Oregon communities of disparate size, location, and demography over a 10-month period. Simultaneously, wastewater SARS-CoV-2 concentrations were quantified at each community’s wastewater treatment plant and from 22 Newport, Oregon, neighborhoods. SARS-CoV-2 RNA was sequenced from all positive wastewater and nasal swab samples. Clinically reported case counts were obtained from the Oregon Health Authority.

Results:

Estimated community SARS-CoV-2 prevalence ranged from 8 to 1,687/10,000 persons. Community wastewater SARS-CoV-2 concentrations ranged from 2.9 to $5.1 log to the base 10$ gene copies per liter. Wastewater SARS-CoV-2 concentrations were more highly correlated (Pearson’s $lowercase italic r equals 0.96$ ; $uppercase italic r squared equals 0.91$ ) with community prevalence than were clinically reported cases of COVID-19 (Pearson’s $lowercase italic r equals 0.85$ ; $uppercase italic r squared equals 0.73$ ). Monte Carlo simulations indicated that wastewater SARS-CoV-2 concentrations were significantly better than clinically reported cases at estimating prevalence ( $lowercase italic p less than 0.05$ ). In addition, wastewater analyses determined neighborhood-level COVID-19 hot spots and identified SARS-CoV-2 variants (B.1 and B.1.399) at the neighborhood and city scales.

Discussion:

The greater reliability of wastewater SARS-CoV-2 concentrations over clinically reported case counts was likely due to systematic biases that affect reported case counts, including variations in access to testing and underreporting of asymptomatic cases. With these advantages, combined with scalability and low costs, wastewater-based epidemiology can be a key component in public health surveillance of COVID-19 and other communicable infections. https://doi.org/10.1289/EHP10289

中文翻译：

基于废水的流行病学方法评估 SARS-CoV-2 感染流行率以及俄勒冈州不同社区城市和社区规模病毒变异体的检测

抽象的

背景：

据报道，废水中的 SARS-CoV-2 浓度与社区的感染、疾病或两者的负担之间存在正相关关系。然而，之前的研究大多将废水与临床病例数或非代表性的方便样本进行比较，限制了它们的定量潜力。

目标：

本研究探讨了废水 SARS-CoV-2 浓度是否可以比报告的 COVID-19 病例更好地估计 SARS-CoV-2 社区患病率。此外，这项研究还测试了基于废水的流行病学方法是否可以识别社区级的 COVID-19 热点和 SARS-CoV-2 变异体。

方法：

社区 SARS-CoV-2 患病率是根据 10 个月内俄勒冈州六个不同规模、地点和人口特征的社区的 8 次随机挨家挨户鼻拭子采样事件估算得出的。同时，对每个社区废水处理厂和俄勒冈州纽波特 22 个社区的废水 SARS-CoV-2 浓度进行了量化。对所有阳性废水和鼻拭子样本中的 SARS-CoV-2 RNA 进行了测序。临床报告的病例数来自俄勒冈州卫生局。

结果：

估计社区 SARS-CoV-2 患病率范围为 8 至 1,687/10,000 人。社区废水中 SARS-CoV-2 浓度范围为 2.9 至 $5.1 {日志}_{10}$ 每升基因拷贝数。废水中 SARS-CoV-2 浓度的相关性更高（Pearson 的 $r = 0.96$ ; $右^{2} = 0.91$ ）的社区患病率高于临床报告的 COVID-19 病例（Pearson 的 $r = 0.85$ ; $右^{2} = 0.73$ ）。蒙特卡罗模拟表明，在估计患病率时，废水中的 SARS-CoV-2 浓度明显优于临床报告的病例（ $p < 0.05$ ）。此外，废水分析确定了社区层面的 COVID-19 热点，并在社区和城市范围内确定了 SARS-CoV-2 变体（B.1 和 B.1.399）。

讨论：

废水 SARS-CoV-2 浓度相对于临床报告病例数的可靠性更高，可能是由于影响报告病例数的系统偏差，包括检测机会的变化和无症状病例的漏报。凭借这些优势，再加上可扩展性和低成本，基于废水的流行病学可以成为 COVID-19 和其他传染病公共卫生监测的关键组成部分。 https://doi.org/10.1289/EHP10289

更新日期：2022-06-29

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