(C) PLOS One [1]. This unaltered content originally appeared in journals.plosone.org.
Licensed under Creative Commons Attribution (CC BY) license.
url:https://journals.plos.org/plosone/s/licenses-and-copyright

------------



Operationalizing a routine wastewater monitoring laboratory for SARS-CoV-2

['Rose S. Kantor', 'Department Of Civil', 'Environmental Engineering', 'University Of California', 'Berkeley', 'California', 'United States Of America', 'Hannah D. Greenwald', 'Lauren C. Kennedy', 'Adrian Hinkle']

Date: 2022-02 

Abstract Wastewater-based testing for SARS-CoV-2 is a novel tool for public health monitoring, but additional laboratory capacity is needed to provide routine monitoring at all locations where it has the potential to be useful. Few standardization practices for SARS-CoV-2 wastewater analysis currently exist, and quality assurance/quality control procedures may vary across laboratories. Alongside counterparts at many academic institutions, we built out a laboratory for routine monitoring of wastewater at the University of California, Berkeley. Here, we detail our group’s establishment of a wastewater testing laboratory including standard operating procedures, laboratory buildout and workflow, and a quality assurance plan. We present a complete data analysis pipeline and quality scoring framework and discuss the data reporting process. We hope that this information will aid others at research institutions, public health departments, and wastewater agencies in developing programs to support wastewater monitoring for public health decision-making.

Citation: Kantor RS, Greenwald HD, Kennedy LC, Hinkle A, Harris-Lovett S, Metzger M, et al. (2022) Operationalizing a routine wastewater monitoring laboratory for SARS-CoV-2. PLOS Water 1(2): e0000007. https://doi.org/10.1371/journal.pwat.0000007 Editor: Silvia Monteiro, Universidade de Lisboa Instituto Superior Tecnico, PORTUGAL Received: July 9, 2021; Accepted: October 19, 2021; Published: February 15, 2022 Copyright: © 2022 Kantor et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability: Data are available in the Supplementary Texts and Tables. Code is available at https://github.com/wastewaterlab/data_analysis. Funding: Funding was received from the Catena Foundation, the Center for Information Technology Research in Service to Society, and the Innovative Genomics Institute to KLN. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing interests: I have read the journal’s policy and the authors of this manuscript have the following competing interests: RSK is a friend of the former Executive Editor of PLOS Water. The remaining authors have declared that no competing interests exist.

1. Introduction Wastewater-based epidemiology (WBE) is a pandemic response tool that provides population-level public health information to complement clinical testing and other epidemiological data [1–5]. At the outset of the coronavirus disease 2019 (COVID-19) pandemic, academic, commercial, and wastewater utility laboratories developed and optimized protocols for concentration, extraction, and quantification of SARS-CoV-2 RNA from wastewater [1, 2, 4, 6–14]. Due to an unprecedented level of collaboration [15], standard operating procedures (SOPs) and commercial kits now enable routine wastewater monitoring. However, in many locales, implementation of WBE is still in the early stages or is housed in academic research laboratories [16]. As wastewater monitoring enters a new phase with the implementation of the Center for Disease Control and Prevention’s National Wastewater Surveillance System (CDC-NWSS) [17], there may be a need to expand the capacity of existing laboratories or establish new ones. There is also an ongoing need for transparency and documentation of raw data analysis methods and quality controls. In particular, quality control for WBE analysis has not been standardized, and conveying the quality of results with multiple analytical controls is complex [18]. Finally, submitting data to CDC-NWSS requires conformation to data field code specifications which can be time-consuming to perform manually. In October 2020, we launched a laboratory at the University of California, Berkeley, to support wastewater monitoring for SARS-CoV-2 in the San Francisco Bay Area. We developed and optimized standard operating procedures, workflows, and a data analysis code base. The main contributions of this work are to provide: 1) a start-to-finish guidance document on laboratory set-up & operation drawn from our experience, 2) a data analysis pipeline for WBE that implements best practices in the field and is compatible with CDC-NWSS, 3) a unique data quality scoring method that can be adapted to meet the needs of other labs using different methodologies. While we recognize that there is no single preferred method or set of methods for analyzing SARS-CoV-2 in wastewater, we hope that these resources will be useful to other groups regardless of which methods are used.

4. Discussion Because the COVID-19 pandemic has spurred widespread application of WBE, we expect that new laboratories will continue to be launched and expanded even after the COVID-19 pandemic. Wastewater monitoring for SARS-CoV-2 requires methods and equipment that may differ from testing wastewater for regulatory compliance and from clinical testing for SARS-CoV-2. In our experience, laboratory set-up required unique considerations for safety, space, workflow, and data management. Additionally, consideration for the scale of the laboratory became important as monitoring needs grew. If warranted, higher throughput than that described here could be achieved via large-volume liquid handling robots for extraction and precision liquid handlers for PCR plate set-up. Several factors influence whether it is most cost-effective and reliable to test samples in smaller, local laboratories versus larger, centralized laboratories. Smaller labs may face higher costs associated with low-throughput analysis, and potential challenges could arise in data comparison among locations. For larger labs, initial costs of robotic equipment and farther shipping with associated longer turnaround times may be issues of concern. Creating a robust network of WBE monitoring laboratories necessitates capacity-building across sectors including public health labs, utility labs, and commercial labs both nationally and internationally. Building a flexible data analysis pipeline allowed us to reproducibly compare data over time and to incorporate elements like LoD substitution for non-detects and calculation of geometric standard error of technical replicates. Analysis pipelines like this one can streamline the submission process to CDC-NWSS, which requires extensive details about each sample. Additionally, the pipeline presented here allowed meta-analysis of the data, revealing the variability present in each step of sample processing. While some amount of variation is due to lower quality or technical error, some appears to be inherent methodological variation or variation in the wastewater itself [26, 27]. In the future, modeling the contributions of these variables to overall noise in the data could provide more confidence in the results. The development of a robust quality assurance plan is critical for any laboratory monitoring SARS-CoV-2 in wastewater. Others have documented the controls and standards required for WBE [18, 27]. Our newly developed quality scoring framework and code represent one possible model for communicating data quality to partners in public health. Quality score parameters, thresholds, and weights were chosen based on our experience and meta-analyses of our data. While these choices are dependent on the methodology used by a lab, the scoring framework itself is adaptable. As wastewater monitoring for SARS-CoV-2 continues to expand as part of managing the COVID-19 pandemic, more academic institutions, wastewater agencies, and public health agencies may choose to analyze wastewater samples from routine monitoring efforts in-house. We hope lessons learned and reported here from our experience of developing a laboratory to routinely monitor wastewater samples for SARS-CoV-2 RNA during the COVID-19 pandemic can assist others with similar goals.

Acknowledgments We gratefully acknowledge the support of many members of our technical laboratory team, including Joaquin Bradley Silva, Oscar Whitney, Vinson Fan, Alma Bartholow, Li-Wen Wang, Anmol Seth, Amita Muralidharan, Constance Chiang, Farheen Jamshed, Christina Lang, Cristina Baily, Karen Lee, Aliya Ehde, Mira Chapin, Sohyun Cho, Owen Zuidema, Avery Parks, Emna Selami, Jazmine Ramos, Annesha Ghosh, Sofia Mireles, and Lauder Fairchok.

[END]

[1] Url: https://journals.plos.org/water/article?id=10.1371/journal.pwat.0000007

(C) Plos One. "Accelerating the publication of peer-reviewed science."
Licensed under Creative Commons Attribution (CC BY 4.0)
URL: https://creativecommons.org/licenses/by/4.0/


via Magical.Fish Gopher News Feeds:
gopher://magical.fish/1/feeds/news/plosone/