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      Establishing a Statewide Wastewater Surveillance System in Response to the COVID-19 Pandemic: A Reliable Model for Continuous and Emerging Public Health Threats

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          Abstract

          Context:

          The COVID-19 pandemic sparked efforts across the globe to implement wastewater surveillance for SARS-CoV-2.

          Program:

          New York State (NYS) established the NYS Wastewater Surveillance Network to estimate the levels of COVID-19 community risk and to provide an early indication of SARS-CoV-2 transmission trends. The network is designed to provide a better understanding of public health burdens and to assist health departments to respond effectively to public health threats.

          Implementation:

          Wastewater surveillance across NYS increased from sporadic and geographically spare in 2020 to routine and widespread in 2022, reaching all 62 counties in the state and covering 74% of New Yorkers. The network team focused on engaging local health departments and wastewater treatment plants to provide wastewater samples, which are then analyzed through a network-affiliated laboratory. Both participating local health departments and wastewater treatment plants receive weekly memos on current SARS-CoV-2 trends and levels. The data are also made publicly available at the state dashboard.

          Evaluation:

          Using standard indicators to evaluate infectious disease surveillance systems, the NYS Wastewater Surveillance Network was assessed for accuracy, timeliness, and completeness during the first year of operations. We observed 96.5% sensitivity of wastewater to identify substantial/high COVID-19 transmission and 99% specificity to identify low COVID-19 transmission. In total, 80% of results were reported within 1 day of sample collection and were published on the public dashboard within 2 days of sample collection. Among participating wastewater treatment plants, 32.5% provided weekly samples with zero missing data, 31% missed 1 or 2 weeks, and 36.5% missed 3 or more weeks.

          Discussion:

          The NYS Wastewater Surveillance Network continues to be a key component of the state and local health departments' pandemic response. The network fosters prompt public health actions through real-time data, enhancing the preparedness capability for both existing and emerging public health threats.

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          Most cited references18

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          Presence of SARS-Coronavirus-2 RNA in Sewage and Correlation with Reported COVID-19 Prevalence in the Early Stage of the Epidemic in The Netherlands

          In the current COVID-19 pandemic, a significant proportion of cases shed SARS-Coronavirus-2 (SARS-CoV-2) with their faeces. To determine if SARS-CoV-2 RNA was present in sewage during the emergence of COVID-19 in The Netherlands, sewage samples of six cities and the airport were tested using four qRT-PCR assays, three targeting the nucleocapsid gene (N1–N3) and one the envelope gene (E). No SARS-CoV-2 RNA was detected on February 6, 3 weeks before the first Dutch case was reported. On March 4/5, one or more gene fragments were detected in sewage of three sites, in concentrations of 2.6–30 gene copies per mL. In Amersfoort, N3 was detected in sewage 6 days before the first cases were reported. As the prevalence of COVID-19 in these cities increased in March, the RNA signal detected by each qRT-PCR assay increased, for N1–N3 up to 790–2200 gene copies per mL. This increase correlated significantly with the increase in reported COVID-19 prevalence. The detection of the virus RNA in sewage, even when the COVID-19 prevalence is low, and the correlation between concentration in sewage and reported prevalence of COVID-19, indicate that sewage surveillance could be a sensitive tool to monitor the circulation of the virus in the population.
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            Quantitative CrAssphage PCR Assays for Human Fecal Pollution Measurement

            Environmental waters are monitored for fecal pollution to protect public health and water resources. Traditionally, general fecal-indicator bacteria are used; however, they cannot distinguish human fecal waste from other animal pollution sources. Recently, a novel bacteriophage, crAssphage, was discovered by metagenomic data mining and reported to be abundant in and closely associated with human fecal waste. To confirm bioinformatic predictions, 384 primer sets were designed along the length of the crAssphage genome. Based on initial screening, two novel crAssphage qPCR assays (CPQ_056 and CPQ_064) were designed and evaluated in reference fecal samples and water matrices. The assays exhibited high specificities (98.6%) when tested against an animal fecal reference library, and crAssphage genetic markers were highly abundant in raw sewage and sewage-impacted water samples. In addition, CPQ_056 and CPQ_064 performance was compared to HF183/BacR287 and HumM2 assays in paired experiments. Findings confirm that viral crAssphage qPCR assays perform at a similar level to well-established bacterial human-associated fecal-source-identification approaches. These new viral-based assays could become important water quality management and research tools.
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              Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

              Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world’s countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.
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                Author and article information

                Contributors
                Journal
                J Public Health Manag Pract
                J Public Health Manag Pract
                JPUMP
                Journal of Public Health Management and Practice
                Wolters Kluwer Health, Inc.
                1078-4659
                1550-5022
                November 2023
                01 August 2023
                : 29
                : 6 , Public Health Surveillance
                : 854-862
                Affiliations
                Department of Public Health at Syracuse University, Syracuse, New York (Ms Neyra and Drs Hill and Larsen); School of Information Studies at Syracuse University, Syracuse, New York (Mr Dunham); New York State Department of Health, Albany, New York (Ms Bennett); and CDC Foundation, Atlanta, Georgia (Ms Bennett).
                Author notes
                [*] Correspondence: David A. Larsen, PhD, MPH, Department of Public Health, Syracuse University, 150 Crouse Dr, 430C White Hall, Syracuse, NY 13244 ( dalarsen@ 123456syr.edu ).
                Author information
                https://orcid.org/0009-0004-3987-7915
                https://orcid.org/0000-0002-4073-6093
                https://orcid.org/0000-0002-1876-6536
                Article
                jpump2906p854
                10.1097/PHH.0000000000001797
                10549888
                37566797
                84efc531-e838-4c31-bc3a-3057245bb410
                © 2023 The Authors. Published by Wolters Kluwer Health, Inc.

                This is an open-access article distributed under the terms of the Creative Commons Attribution-Non Commercial-No Derivatives License 4.0 (CCBY-NC-ND), where it is permissible to download and share the work provided it is properly cited. The work cannot be changed in any way or used commercially without permission from the journal.

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                health security,infectious disease surveillance,pandemic preparedness,wastewater surveillance

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