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Abstract As clinical testing declines, wastewater monitoring can provide crucial surveillance on the emergence of SARS-CoV-2 variant of concerns (VoCs) in communities. In this paper we present QuaID, a novel bioinformatics tool for VoC detection based on quasi-unique mutations. The benefits of QuaID are three-fold: (i) provides up to 3-week earlier VoC detection, (ii) accurate VoC detection (>95% precision on simulated benchmarks), and (iii) leverages all mutational signatures (including insertions & deletions). 

Wastewater-based epidemiology has played a significant role in monitoring the COVID-19 pandemic, yet little is known about degradation of SARS-CoV-2 in sewer networks. Here, we used advanced sewershed modeling software to simulate SARS-CoV-2 RNA degradation in sewersheds across Houston, TX under various temperatures and decay rates. Moreover, a novel metric, population times travel time ( PT ), was proposed to identify localities with a greater likelihood of undetected COVID-19 outbreaks and to aid in the placement of upstream samplers. Findings suggest that travel time has a greater influence on RNA degradation across the sewershed as compared to temperature. SARS-CoV-2 RNA degradation at median travel times was approximately two times greater in 20 °C wastewater between the small sewershed, Chocolate Bayou, and the larger sewershed, 69th Street. Lastly, placement of upstream samplers according to the PT metric can provide a more representative snapshot of disease incidence in large sewersheds. This study helps to elucidate discrepancies between SARS-CoV-2 viral load in wastewater and clinical incidence of COVID-19. Incorporating travel time and SARS-CoV-2 RNA decay can improve wastewater surveillance efforts. 

The rapid diversification of synthetic biology tools holds promise in making some classically hard-to-solve environmental problems tractable. Here we review longstanding problems in the Earth and environmental sciences that could be addressed using engineered microbes as micron-scale sensors (biosensors). Biosensors can offer new perspectives on open questions, including understanding microbial behaviors in heterogeneous matrices like soils, sediments, and wastewater systems, tracking cryptic element cycling in the Earth system, and establishing the dynamics of microbe-microbe, microbe-plant, and microbe-material interactions. Before these new tools can reach their potential, however, a suite of biological parts and microbial chassis appropriate for environmental conditions must be developed by the synthetic biology community. This includes diversifying sensing modules to obtain information relevant to environmental questions, creating output signals that allow dynamic reporting from hard-to-image environmental materials, and tuning these sensors so that they reliably function long enough to be useful for environmental studies. Finally, ethical questions related to the use of synthetic biosensors in environmental applications are discussed. 

SARS-CoV-2 RNA detection in wastewater is being rapidly developed and adopted as a public health monitoring tool worldwide. With wastewater surveillance programs being implemented across many different scales and by many different stakeholders, it is critical that data collected and shared are accompanied by an appropriate minimal amount of meta-information to enable meaningful interpretation and use of this new information source and intercomparison across datasets. While some databases are being developed for specific surveillance programs locally, regionally, nationally, and internationally, common globally-adopted data standards have not yet been established within the research community. Establishing such standards will require national and international consensus on what meta-information should accompany SARS-CoV-2 wastewater measurements. To establish a recommendation on minimum information to accompany reporting of SARS-CoV-2 occurrence in wastewater for the research community, the United States National Science Foundation (NSF) Research Coordination Network on Wastewater Surveillance for SARS-CoV-2 hosted a workshop in February 2021 with participants from academia, government agencies, private companies, wastewater utilities, public health laboratories, and research institutes. This report presents the primary two outcomes of the workshop: (i) a recommendation on the set of minimum meta-information that is needed to confidently interpret wastewater SARS-CoV-2 data, and (ii) insights from workshop discussions on how to improve standardization of data reporting.