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1. Virus reduction during advanced Bardenpho and conventional wastewater treatment processes

   Schmitz, B. ; Kitajima, M. ; Campillo, M. ; Gerba, C. ; Pepper, I. ( January 2016 , Environmental science & technology)

   The present study investigated wastewater treatment for the removal of 11 different virus types (pepper mild mottle virus; Aichi virus; genogroup I, II, and IV noroviruses; enterovirus;sapovirus; group-A rotavirus; adenovirus; and JC and BK polyomaviruses) by two wastewater treatment facilities utilizing advanced Bardenpho technology and compared the results with conventional treatment processes. To our knowledge, this is the first study comparing full-scale treatment processes that all received sewage influent from the same region. The incidence of viruses in wastewater was assessed with respect to absolute abundance, occurrence, and reduction in monthly samples collected throughout a 12 month period in southern Arizona. Samples were concentrated via an electronegative filter method and quantified using TaqMan-based quantitative polymerase chain reaction (qPCR). Results suggest that Plant D, utilizing an advanced Bardenpho process as secondary treatment, effectively reduced pathogenic viruses better than facilities using conventional processes. However, the absence of cell-culture assays did not allow an accurate assessment of infective viruses. On the basis of these data, the Aichi virus is suggested as a conservative viral marker for adequate wastewater treatment, as it most often showed the best correlation coefficients to viral pathogens, was always detected at higher concentrations, and may overestimate the potential virus risk. 

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2. Fate of the Urinary Tract Virus BK Human Polyomavirus in Source-Separated Urine

   https://doi.org/10.1128/AEM.02374-17  

   Goetsch, Heather E. ; Zhao, Linbo ; Gnegy, Mariah ; Imperiale, Michael J. ; Love, Nancy G. ; Wigginton, Krista R. ; Elkins, Christopher A. ( April 2018 , Applied and Environmental Microbiology)

   ABSTRACT Human polyomaviruses are emerging pathogens that infect a large percentage of the human population and are excreted in urine. Consequently, urine that is collected for fertilizer production often has high concentrations of polyomavirus genes. We studied the fate of infectious double-stranded DNA (dsDNA) BK human polyomavirus (BKPyV) in hydrolyzed source-separated urine with infectivity assays and quantitative PCR (qPCR). Although BKPyV genomes persisted in the hydrolyzed urine for long periods of time ( T 90 [time required for 90% reduction in infectivity or gene copies] of >3 weeks), the viruses were rapidly inactivated ( T 90 of 1.1 to 11 h) in most of the tested urine samples. Interestingly, the infectivity of dsDNA bacteriophage surrogate T3 ( T 90 of 24 to 46 days) was much more persistent than that of BKPyV, highlighting a major shortcoming of using bacteriophages as human virus surrogates. Pasteurization and filtration experiments suggest that BKPyV virus inactivation was due to microorganism activity in the source-separated urine, and SDS-PAGE Western blots showed that BKPyV protein capsid disassembly is concurrent with inactivation. Our results imply that stored urine does not pose a substantial risk of BKPyV transmission, that qPCR and infectivity of the dsDNA surrogate do not accurately depict BKPyV fate, and that microbial inactivation is driven by structural elements of the BKPyV capsid. IMPORTANCE We demonstrate that a common urinary tract virus has a high susceptibility to the conditions in hydrolyzed urine and consequently would not be a substantial exposure route to humans using urine-derived fertilizers. The results have significant implications for understanding virus fate. First, by demonstrating that the dsDNA (double-stranded DNA) genome of the polyomavirus lasts for weeks despite infectivity lasting for hours to days, our work highlights the shortcomings of using qPCR to estimate risks from unculturable viruses. Second, commonly used dsDNA surrogate viruses survived for weeks under the same conditions that BK polyomavirus survived for only hours, highlighting issues with using virus surrogates to predict how human viruses will behave in the environment. Finally, our mechanistic inactivation analysis provides strong evidence that microbial activity drives rapid virus inactivation, likely through capsid disassembly. Overall, our work underlines how subtle structural differences between viruses can greatly impact their environmental fate. 

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3. Transcriptomic and rRNA:rDNA Signatures of Environmental versus Enteric Enterococcus faecalis Isolates under Oligotrophic Freshwater Conditions

   https://doi.org/10.1128/Spectrum.00817-21  

   Suttner, Brittany ; Kim, Minjae ; Johnston, Eric R. ; Orellana, Luis H. ; Ruiz-Perez, Carlos A. ; Rodriguez-R, Luis M. ; Hatt, Janet K. ; Brown, Joe ; Santo Domingo, Jorge W. ; Konstantinidis, Konstantinos T. ( October 2021 , Microbiology Spectrum)

   Gralnick, Jeffrey A. (Ed.)

   ABSTRACT The use of enterococci as a fecal indicator bacterial group for public health risk assessment has been brought into question by recent studies showing that “naturalized” populations of Enterococcus faecalis exist in the extraenteric environment. The extent to which these naturalized E. faecalis organisms can confound water quality monitoring is unclear. To determine if strains isolated from different habitats display different survival strategies and responses, we compared the decay patterns of three E. faecalis isolates from the natural environment (environmental strains) against three human gut isolates (enteric strains) in laboratory mesocosms that simulate an oligotrophic, aerobic freshwater environment. Our results showed similar overall decay rates between enteric and environmental isolates based on viable plate and quantitative PCR (qPCR) counts. However, the enteric isolates exhibited a spike in copy number ratios of 16S rRNA gene transcripts to 16S rRNA gene DNA copies (rRNA:rDNA ratios) between days 1 and 3 of the mesocosm incubations that was not observed in environmental isolates, which could indicate a different stress response. Nevertheless, there was no strong evidence of differential gene expression between environmental and enteric isolates related to habitat adaptation in the accompanying mesocosm metatranscriptomes. Overall, our results provide novel information on how rRNA levels may vary over different growth conditions (e.g., standard lab versus oligotrophic) for this important indicator bacteria. We also observed some evidence for habitat adaptation in E. faecalis ; however, this adaptation may not be substantial or consistent enough for integration in water quality monitoring. IMPORTANCE Enterococci are commonly used worldwide to monitor environmental fecal contamination and public health risk for waterborne diseases. However, closely related enterococci strains adapted to living in the extraenteric environment may represent a lower public health risk and confound water quality estimates. We developed an rRNA:rDNA viability assay for E. faecalis (a predominant species within this fecal group) and tested it against both enteric and environmental isolates in freshwater mesocosms to assess whether this approach can serve as a more sensitive water quality monitoring tool. We were unable to reliably distinguish the different isolate types using this assay under the conditions tested; thus, environmental strains should continue to be counted during routine water monitoring. However, this assay could be useful for distinguishing more recent (i.e., higher-risk) fecal pollution because rRNA levels significantly decreased after 1 week in all isolates. 

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4. Quantification of Evapotranspiration and Water Chemistry in a Remediated Wetland in Everglades National Park, USA

   https://doi.org/10.3390/w15040611  

   Reio, Dillon Nicholas ; Price, René M. ; Melesse, Assefa M. ; Ross, Michael ( February 2023 , Water)

   Similar to most wetlands, the Florida Everglades landscape was altered to promote agriculture and human settlement, significantly altering the natural hydrologic regime. Once former agricultural land located within Everglades National Park (ENP), the Hole-in-the-Donut (HID) wetland restoration program became the first mitigation bank project in Florida. The HID program utilized a restoration technique of complete soil removal to effectively eradicate an invasive plant species. This research investigated the effects of the vegetation and soil removal on the hydrologic conditions of the HID, specifically evapotranspiration and water chemistry. Annual evapotranspiration rates were determined for the region using remotely sensed data and compared to the acres restored over a 15-year period. Groundwater and surface waters were collected from both inside the HID and from adjacent areas within ENP for major cations and anions and total nutrient concentrations. Evapotranspiration rates were found to decrease from a mean of 1083.4 mm year−1 in the year 2000 to 891.6 mm year−1 in 2014 as the restored area increased to 4893 acres. Concentrations of ions and nutrients were lower in groundwater and surface water within the restored areas compared to adjacent areas. We conclude that the lack of soil cover (along with reduced evapotranspiration rates) contributed to the lower ion and nutrient concentrations in the surface water and groundwater within the HID. 

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5. Direct detection of human adenovirus or SARS-CoV-2 with ability to inform infectivity using DNA aptamer-nanopore sensors

   https://doi.org/10.1126/sciadv.abh2848  

   Peinetti, Ana S. ; Lake, Ryan J. ; Cong, Wen ; Cooper, Laura ; Wu, Yuting ; Ma, Yuan ; Pawel, Gregory T. ; Toimil-Molares, María Eugenia ; Trautmann, Christina ; Rong, Lijun ; et al ( September 2021 , Science Advances)

   Viral infections are a major global health issue, but no current method allows rapid, direct, and ultrasensitive quantification of intact viruses with the ability to inform infectivity, causing misdiagnoses and spread of the viruses. Here, we report a method for direct detection and differentiation of infectious from noninfectious human adenovirus and SARS-CoV-2, as well as from other virus types, without any sample pretreatment. DNA aptamers are selected from a DNA library to bind intact infectious, but not noninfectious, virus and then incorporated into a solid-state nanopore, which allows strong confinement of the virus to enhance sensitivity down to 1 pfu/ml for human adenovirus and 1 × 10 4 copies/ml for SARS-CoV-2. Applications of the aptamer-nanopore sensors in different types of water samples, saliva, and serum are demonstrated for both enveloped and nonenveloped viruses, making the sensor generally applicable for detecting these and other emerging viruses of environmental and public health concern. 

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