Microbiome Analysis for Wastewater Surveillance during COVID-19
Kyle D. Brumfield,Menu B. Leddy,M. Usmani,Joseph A. Cotruvo,Ching-Tzone Tien,Suzanne Dorsey,Karlis Graubics,B. Fanelli,Isaac Zhou,Nathaniel Registe,Manoj Dadlani,Malinda Wimalarante,Dilini Jinasena,Rushan Abayagunawardena,Chiran Withanachchi,Anwar Huq,Antarpreet Jutla,Rita R. Colwell +17 more
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TL;DR: The wastewater microbiome provides useful public health information, and hence, a valuable tool to proactively detect and characterize pathogenic agents circulating in a community, and metagenomics of wastewater can serve as an early warning system for communicable diseases.
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Abstract: Traditionally, testing for COVID-19 is done by detecting SARS-CoV-2 in samples collected from nasal swabs and/or saliva. However, SARS-CoV-2 can also be detected in feces of infected individuals. ABSTRACT Wastewater surveillance (WS), when coupled with advanced molecular techniques, offers near real-time monitoring of community-wide transmission of SARS-CoV-2 and allows assessing and mitigating COVID-19 outbreaks, by evaluating the total microbial assemblage in a community. Composite wastewater samples (24 h) were collected weekly from a manhole between December 2020 and November 2021 in Maryland, USA. RT-qPCR results showed concentrations of SARS-CoV-2 RNA recovered from wastewater samples reflected incidence of COVID-19 cases. When a drastic increase in COVID-19 was detected in February 2021, samples were selected for microbiome analysis (DNA metagenomics, RNA metatranscriptomics, and targeted SARS-CoV-2 sequencing). Targeted SARS-CoV-2 sequencing allowed for detection of important genetic mutations, such as spike: K417N, D614G, P681H, T716I, S982A, and D1118H, commonly associated with increased cell entry and reinfection. Microbiome analysis (DNA and RNA) provided important insight with respect to human health-related factors, including detection of pathogens and their virulence/antibiotic resistance genes. Specific microbial species comprising the wastewater microbiome correlated with incidence of SARS-CoV-2 RNA, suggesting potential association with SARS-CoV-2 infection. Climatic conditions, namely, temperature, were related to incidence of COVID-19 and detection of SARS-CoV-2 in wastewater, having been monitored as part of an environmental risk score assessment carried out in this study. In summary, the wastewater microbiome provides useful public health information, and hence, a valuable tool to proactively detect and characterize pathogenic agents circulating in a community. In effect, metagenomics of wastewater can serve as an early warning system for communicable diseases, by providing a larger source of information for health departments and public officials. IMPORTANCE Traditionally, testing for COVID-19 is done by detecting SARS-CoV-2 in samples collected from nasal swabs and/or saliva. However, SARS-CoV-2 can also be detected in feces of infected individuals. Therefore, wastewater samples can be used to test all individuals of a community contributing to the sewage collection system, i.e., the infrastructure, such as gravity pipes, manholes, tanks, lift stations, control structures, and force mains, that collects used water from residential and commercial sources and conveys the flow to a wastewater treatment plant. Here, we profile community wastewater collected from a manhole, detect presence of SARS-CoV-2, identify genetic mutations of SARS-CoV-2, and perform COVID-19 risk score assessment of the study area. Using metagenomics analysis, we also detect other microorganisms (bacteria, fungi, protists, and viruses) present in the samples. Results show that by analyzing all microorganisms present in wastewater, pathogens circulating in a community can provide an early warning for contagious diseases.
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Citations
Wastewater-based surveillance as a tool for public health action: SARS-CoV-2 and beyond
Michael D. Parkins,Bonita Lee,Nicole Acosta,Maria Bautista,Casey R J Hubert,Steve Hrudey,Kevin Frankowski,Xiao-Li Pang +7 more
TL;DR: A state-of-the-art review of WBS as established with SARS-CoV-2 is provided and the current work underway expanding its scope to other infectious disease targets is details.
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TL;DR: In this paper , the authors investigated the utility of near-source wastewater surveillance for the detection of local influenza transmission in schools, which has the potential to be investigated further with paired school-level influenza incidence data.
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Yanmei Zhao,Fa Yuan Huang,Wenxiu Wang,Rui Gao,Lu Fan,Aijie Wang,Shuyan Gao +6 more
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