A multi-population-based genomic analysis uncovers unique haplotype variants and crucial mutant genes in SARS-CoV-2.

BACKGROUND: COVID-19 is a disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Rigorous detection and treatment strategies against SARS-CoV-2 have become very challenging due to continuous evolutions to the viral genome. Therefore, careful genomic analysis is sorely needed to understand transmission, the cellular mechanism of pathogenicity, and the development of vaccines or drugs. OBJECTIVE: In this study, we intended to identify SARS-CoV-2 genome variants that may help understand the cellular and molecular foundation of coronavirus infections required to develop effective intervention strategies. METHODS: SARS-CoV-2 genome sequences were downloaded from an open-source public database, processed, and analyzed for variants in target detection sites and genes. RESULTS: We have identified six unique variants, G---AAC, T---AAC---T, AAC---T, AAC--------T, C----------T, and C--------C, at the nucleocapsid region and eleven major hotspot mutant genes: nsp3, surface glycoprotein, nucleocapsid phosphoprotein, ORF8, nsp6, nsp2, nsp4, helicase, membrane glycoprotein, 3'-5' exonuclease, and 2'-O-ribose methyltransferases. In addition, we have identified eleven major mutant genes that may have a crucial role in SARS-CoV-2 pathogenesis. CONCLUSION: Studying haplotype variants and 11 major mutant genes to understand the mechanism of action of fatal pathogenicity and inter-individual variations in immune responses is inevitable for managing target patient groups with identified variants and developing effective anti-viral drugs and vaccines.

Municipal reclaimed water for multi-purpose applications in the power sector: A review.

Wastewater and power utilities in the United States have an enormous opportunity to collaborate on the mutually beneficial uses of reclaimed water. Despite close proximity to wastewater facilities, only a limited number of power plants are currently using municipal reclaimed water for cooling tower and boiler applications. Through a review of the literature, this document aims at creating a more perspicuous understanding of the reuse of reclaimed water for power plant applications, particularly as pertains to those associated with cooling towers and boilers, by highlighting the drivers of current implementation, regulatory issues and treatment goals, and available treatment technologies. Through an in-depth analysis of case studies, the review also highlights key examples of reclaimed water reuse projects at power utilities together with the related benefits and challenges.

Recent innovations and trends in in-conduit hydropower technologies and their applications in water distribution systems.

Water conduits have a large untapped potential to recapture energy for small hydroelectric generation, which can substantially reduce grid electricity consumption and/or provide renewable energy to water agencies. Over the past decade, there has been a recent technological renaissance in off-the-shelf "water-to-wire" turbine technologies including reaction, impulse, and hydrokinetic turbines that target the sub 1-MW in-conduit hydroelectric market. However, adoption of small hydropower technologies remain limited in water and wastewater utility sector, possibly due to the lack of market penetration and exposure. Moreover, information about newly developed small hydropower technologies in the last 5-10 years for in-conduit applications are highly dispersed in the literature. As such, this paper is a comprehensive review on recent technological innovations and trends in hydropower generation from water conduits. Sixteen turbine technologies (eight conventional turbines and eight emerging turbines) are assessed and compared based on their potential benefits and challenges, technology readiness levels, as well as potential sites for installations in diversion structures, potable and irrigation water distribution systems, and wastewater outfalls. Although conventional turbines are considered to be more robust, the modular design of the newer turbines potentially offers a more cost effective solution and better scaling-up capability. Selected case studies on the application of conventional and new turbines for pipelines are also are also reviewed and discussed.

Minimizing Energy Use and GHG Emissions of Lift Stations Utilizing Real-Time Pump Control Strategies.

Wastewater collection system lift station operations require a substantial amount of energy, and can be as a major source of greenhouse gas (GHG) emissions for wastewater utilities. Many lift stations operate with local or basic controls that have no hydraulic relationship with other collection system lift stations. This study demonstrated a unique energy-efficient control method of lift station operation that utilizes hydraulic modeling results generated from site-specific conditions to optimize the pumping units and reduce simultaneous running cycles on a real time basis. The pilot tests conducted at two pilot areas of the wastewater collection system of a utility in Florida demonstrated that the energy savings obtained through such operational optimization was 14 to 17% for the two pilot areas investigated. The study demonstrated that substantial annual energy costs and GHG emissions reduction could be achieved utilizing this method, particularly for utilities located in flat geographic locations where hundreds of lift stations are required to transfer wastewater.

Investigation of Cost and Energy Optimization of Drinking Water Distribution Systems.

Holistic management of water and energy resources through energy and water quality management systems (EWQMSs) have traditionally aimed at energy cost reduction with limited or no emphasis on energy efficiency or greenhouse gas minimization. This study expanded the existing EWQMS framework and determined the impact of different management strategies for energy cost and energy consumption (e.g., carbon footprint) reduction on system performance at two drinking water utilities in California (United States). The results showed that optimizing for cost led to cost reductions of 4% (Utility B, summer) to 48% (Utility A, winter). The energy optimization strategy was successfully able to find the lowest energy use operation and achieved energy usage reductions of 3% (Utility B, summer) to 10% (Utility A, winter). The findings of this study revealed that there may be a trade-off between cost optimization (dollars) and energy use (kilowatt-hours), particularly in the summer, when optimizing the system for the reduction of energy use to a minimum incurred cost increases of 64% and 184% compared with the cost optimization scenario. Water age simulations through hydraulic modeling did not reveal any adverse effects on the water quality in the distribution system or in tanks from pump schedule optimization targeting either cost or energy minimization.

Energy and water quality management systems for water utility's operations: a review.

Holistic management of water and energy resources is critical for water utilities facing increasing energy prices, water supply shortage and stringent regulatory requirements. In the early 1990s, the concept of an integrated Energy and Water Quality Management System (EWQMS) was developed as an operational optimization framework for solving water quality, water supply and energy management problems simultaneously. Approximately twenty water utilities have implemented an EWQMS by interfacing commercial or in-house software optimization programs with existing control systems. For utilities with an installed EWQMS, operating cost savings of 8-15% have been reported due to higher use of cheaper tariff periods and better operating efficiencies, resulting in the reduction in energy consumption of ∼6-9%. This review provides the current state-of-knowledge on EWQMS typical structural features and operational strategies and benefits and drawbacks are analyzed. The review also highlights the challenges encountered during installation and implementation of EWQMS and identifies the knowledge gaps that should motivate new research efforts.

Impact of environmental conditions on the suitability of microconstituents as markers for determining nutrient loading from reclaimed water.

Nitrogen and phosphorous loading into waterways from designated beneficial uses of reclaimed water is a growing concern in many parts of the United States. Numerous studies have documented that organic microconstituents present in the reclaimed water can be utilized as indicators of its influence on surface water bodies. However, little to no information is available on the environmental attenuation of these microconstituents relative to the nutrients, which is a critical component in determining the effectiveness or limitations of those markers as a tool for elucidating their origins. In this study, the stability of selected markers (sucralose, carbamazepine, gadolinium anomaly, iohexol, and atenolol) was evaluated through bench-scale studies designed to simulate environmental conditions associated with biodegradation, adsorption, and photolysis. The primary pathway for nitrogen reduction was biodegradation (greater than 99%) while the highest phosphorous removal was due to adsorption (30-80%). Soils with low organic content were selected for this study. Sucralose was the most recalcitrant microconstituent in the environment with less than 15% removal by adsorption, biodegradation, or photolysis. Iohexol was too susceptible to photolysis (90% removal), and atenolol was susceptible to biodegradation (60-80% removal). Gd anomaly was fairly stable (less than 30% removal) in the environment. Carbamazepine was another efficacious marker for wastewater, but was susceptible (50% removal) to photolysis. Of the selected microconstituents, only atenolol showed any similarity with the attenuation observed for nitrate and none of the microconstituents showed any similarity with the attenuation observed for phosphorus.

Differentiating sources of anthropogenic loading to impaired water bodies utilizing ratios of sucralose and other microconstituents.

Previous studies have suggested the use of sucralose, a synthetic non-nutritive sweetener, as an indicator of domestic wastewater loading to surface waters. This paper presents a novel flow schematic approach for quantifying volumetric load contributions from different water sources by utilizing sucralose as a master diagnostic variable in combination with other trace compounds. This conceptual approach was validated through demonstration of sucralose presence at positive field sites susceptible to either water reuse or septic infiltration and its absence at negative field sites. Differences in the ratios of carbamazepine to sucralose and gadolinium anomaly to sucralose were demonstrated for eight septic and water reuse effluents. Utilization of these ratios as a means of distinguishing septic and water reuse loading to water bodies merits additional study. In the absence of sustained loading, the use of carbamazepine might be hindered by photolysis and gadolinium anomaly might be hindered when volumetric loading is less than 20%.

Sources of nutrients impacting surface waters in Florida: a review.

The promulgation of numeric nutrient criteria for evaluating impairment of waterbodies in Florida is underway. Adherence to the water quality standards needed to meet these criteria will potentially require substantial allocations of public and private resources in order to better control nutrient (i.e., nitrogen and phosphorus) releases from contributing sources. Major sources of nutrients include atmospheric deposition (195-380 mg-N/m(2)/yr, 6 to 16 mg-P/m(2)/yr), reclaimed water irrigation (0.13-29 mg-N/L, 0.02 to 6 mg-P/L), septic systems (3.3 × 10(3)-6.68 × 10(3) g-N/person/yr, 0.49 × 10(3)-0.85 × 10(3) g-P/person/yr) and fertilizer applications (8 × 10(6)-24 × 10(6) mg-N/m(2)/yr). Estimated nitrogen loadings to the Florida environment, as calculated from the above rates are as follows: 5.9 × 10(9)-9.4 × 10(9) g-N/yr from atmospheric deposition, 1.2 × 10(8)-2.6 × 10(10) g-N/yr from reclaimed water, 2.4 × 10(10)-4.9 × 10(10) g-N/year from septic systems, and 1.4 × 10(11) g-N/yr from fertilizer application. Similarly, source specific phosphorus loading calculations are also presented in this paper. A fraction of those nutrient inputs may reach receiving waterbodies depending upon site specific regulation on nutrient control, nutrient management practices, and environmental attenuation. In Florida, the interconnectivity of hydrologic pathways due to the karst landscape and high volumes of rainfall add to the complexity of tracking nutrient loads back to their sources. In addition to source specific nutrient loadings, this review discusses the merits of source specific markers such as elemental isotopes (boron, nitrogen, oxygen, strontium, uranium and carbon) and trace organic compounds (sucralose, gadolinium anomaly, carbamazepine, and galaxolide) in relating nutrient loads back to sources of origin. Although this review is focused in Florida, the development of source specific markers as a tool for tracing nutrient loadings back to sources of origin is applicable and of value to all other geographical locations.

Occurrence and suitability of sucralose as an indicator compound of wastewater loading to surface waters in urbanized regions.

Urban watersheds are susceptible to numerous pollutant sources and the identification of source-specific indicators can provide a beneficial tool in the identification and control of input loads, often times needed for a water body to achieve designated beneficial uses. Differentiation of wastewater flows from other urban wet weather flows is needed in order to more adequately address such environmental concerns as water body nutrient impairment and potable source water contamination. Anthropogenic compounds previously suggested as potential wastewater indicators include caffeine, carbamazepine, N,N-diethyl-meta-toluamide (DEET), gemfibrozil, primidone, sulfamethoxazole, and TCEP. This paper compares the suitability of a variety of anthropogenic compounds to sucralose, an artificial sweetener, as wastewater indicators by examining occurrence data for 85 trace organic compounds in samples of wastewater effluents, source waters with known wastewater point source inputs, and sources without known wastewater point source inputs. The findings statistically demonstrate the superior performance of sucralose as a potential indicator of domestic wastewater input in the U.S. While several compounds were detected in all of the wastewater effluent samples, only sucralose was consistently detected in the source waters with known wastewater discharges, absent in the sources without wastewater influence, and consistently present in septic samples. All of the other compounds were prone to either false negatives or false positives in the environment.

Energy minimization strategies and renewable energy utilization for desalination: a review.

Energy is a significant cost in the economics of desalinating waters, but water scarcity is driving the rapid expansion in global installed capacity of desalination facilities. Conventional fossil fuels have been utilized as their main energy source, but recent concerns over greenhouse gas (GHG) emissions have promoted global development and implementation of energy minimization strategies and cleaner energy supplies. In this paper, a comprehensive review of energy minimization strategies for membrane-based desalination processes and utilization of lower GHG emission renewable energy resources is presented. The review covers the utilization of energy efficient design, high efficiency pumping, energy recovery devices, advanced membrane materials (nanocomposite, nanotube, and biomimetic), innovative technologies (forward osmosis, ion concentration polarization, and capacitive deionization), and renewable energy resources (solar, wind, and geothermal). Utilization of energy efficient design combined with high efficiency pumping and energy recovery devices have proven effective in full-scale applications. Integration of advanced membrane materials and innovative technologies for desalination show promise but lack long-term operational data. Implementation of renewable energy resources depends upon geography-specific abundance, a feasible means of handling renewable energy power intermittency, and solving technological and economic scale-up and permitting issues.

Characterization of microbial populations in pilot-scale fluidized-bed reactors treating perchlorate- and nitrate-laden brine.

A salt-tolerant, perchlorate- and nitrate-reducing bacterial culture developed previously was used to inoculate two acetate-fed fluidized bed reactors (FBRs) which treated a 6% ion-exchange regenerant brine containing 500 +/- 84 mg-N/L nitrate and 4.6 +/- 0.6 mg/L perchlorate. The reactors were operated in series in continuous flow mode for 107 days after an acclimation period of 65 days. Pilot operation data suggest that complete denitrification was achieved after 70 days of operation, but significant perchlorate removal was not observed. Molecular analysis of the inoculum culture and biomass from the pilot plant samples using denaturing gradient gel electrophoresis (DGGE) and fluorescence in situ hybridization (FISH) revealed that the composition of the biomass in the pilot-plant was evolving with time in each FBR. The total number of Azoarcus/Denitromonas decreased in the first reactor with time and position in the bioreactor during acclimation and operation. FISH analysis clearly revealed that the number of Halomonas which was the dominant nitrate-reducing organism increased in the first reactor. This indicates a shift towards nitrate reduction which corresponds to the operation data. Both DGGE and FISH demonstrated that the Azoarcus/Denitromonas was still present in the second bioreactor, which indicated that the removal of nitrate in the first reactor was allowing the perchlorate-reducing organisms to establish themselves in the second reactor. The study also suggests that FISH was more effective for analysis of the composition of these cultures and it would be a better tool for the routine monitoring of cultures.

Kinetics of nitrate and perchlorate reduction in ion-exchange brine using the membrane biofilm reactor (MBfR).

Several sources of bacterial inocula were tested for their ability to reduce nitrate and perchlorate in synthetic ion-exchange spent brine (30-45 g/L) using a hydrogen-based membrane biofilm reactor (MBfR). Nitrate and perchlorate removal fluxes reached as high as 5.4 g Nm(-2)d(-1) and 5.0 g ClO(4)m(-2)d(-1), respectively, and these values are similar to values obtained with freshwater MBfRs. Nitrate and perchlorate removal fluxes decreased with increasing salinity. The nitrate fluxes were roughly first order in H(2) pressure, but roughly zero-order with nitrate concentration. Perchlorate reduction rates were higher with lower nitrate loadings, compared to high nitrate loadings; this is a sign of competition for H(2). Nitrate and perchlorate reduction rates depended strongly on the inoculum. An inoculum that was well acclimated (years) to nitrate and perchlorate gave markedly faster removal kinetics than cultures that were acclimated for only a few months. These results underscore that the most successful MBfR bioreduction of nitrate and perchlorate in ion-exchange brine demands a well-acclimated inoculum and sufficient hydrogen availability.

Perchlorate and nitrate treatment by ion exchange integrated with biological brine treatment.

Groundwater contaminated with perchlorate and nitrate was treated in a pilot plant using a commercially available ion exchange (IX) resin. Regenerant brine concentrate from the IX process, containing high perchlorate and nitrate, was treated biologically and the treated brine was reused in IX resin regeneration. The nitrate concentration of the feed water determined the exhaustion lifetime (i.e., regeneration frequency) of the resin; and the regeneration condition was determined by the perchlorate elution profile from the exhausted resin. The biological brine treatment system, using a salt-tolerant perchlorate- and nitrate-reducing culture, was housed in a sequencing batch reactor (SBR). The biological process consistently reduced perchlorate and nitrate concentrations in the spent brine to below the treatment goals of 500 microg ClO4(-)/L and 0.5mg NO3(-)-N/L determined by equilibrium multicomponent IX modeling. During 20 cycles of regeneration, the system consistently treated the drinking water to below the MCL of nitrate (10 mgNO3(-)-N/L) and the California Department of Health Services (CDHS) notification level of perchlorate (i.e., 6 microg/L). A conceptual cost analysis of the IX process estimated that perchlorate and nitrate treatment using the IX process with biological brine treatment to be approximately 20% less expensive than using the conventional IX with brine disposal.

Beneficial phosphate recovery from reverse osmosis (RO) concentrate of an integrated membrane system using polymeric ligand exchanger (PLE).

Phosphorus (P) discharge to surface water is a major environmental problem. Wastewater treatment is targeted towards removal of this nutrient to prevent degradation of surface water. Integrated membrane systems (IMS) are increasingly being considered for wastewater reclamation, and provide excellent removal of P compounds. However, reverse osmosis (RO), which forms an integral part of these IMSs, concentrates most dissolved substances including P-species such as phosphates in the RO waste stream. In this study, removal of phosphate from this stream using polymeric ligand exchange (PLE) resins was investigated. Further, the possibility of phosphate recovery through struvite (MgNH(4)PO(4).6H(2)O) precipitation was tested. Struvite has been promoted as a slow release fertilizer in recent years. This study demonstrates that PLEs can be successfully used to remove phosphate from RO-concentrate, and to recover more than 85% of the adsorbed phosphorus from the exhausted media and precipitated as a beneficial product (struvite). The approach, presented in this study, suggests advantages of providing economic benefit from a waste product (RO) while avoiding phosphorus discharge to the environment.

Intraparticle diffusion and adsorption of arsenate onto granular ferric hydroxide (GFH).

Porous iron oxides are being evaluated and selected for arsenic removal in potable water systems. Granular ferric hydroxide, a typical porous iron adsorbent, is commercially available and frequently considered in evaluation of arsenic removal methods. GFH is a highly porous (micropore volume approximately 0.0394+/-0.0056 cm(3)g(-1), mesopore volume approximately 0.0995+/-0.0096 cm(3)g(-1)) adsorbent with a BET surface area of 235+/-8 m(2)g(-1). The purpose of this paper is to quantify arsenate adsorption kinetics on GFH and to determine if intraparticle diffusion is a rate-limiting step for arsenic removal in packed-bed treatment systems. Data from bottle-point isotherm and differential column batch reactor (DCBR) experiments were used to estimate Freundlich isotherm parameters (K and 1/n) as well as kinetic parameters describing mass transfer resistances due to film diffusion (k(f)) and intraparticle surface diffusion (D(s)). The pseudo-equilibrium (18 days of contact time) arsenate adsorption density at pH 7 was 8 microg As/mg dry GFH at a liquid phase arsenate concentration of 10 microg As/L. The homogeneous surface diffusion model (HSDM) was used to describe the DCBR data. A non-linear relationship (D(S)=3.0(-9) x R(p)(1.4)) was observed between D(s) and GFH particle radius (R(P)) with D(s) values ranging from 2.98 x 10(-12) cm(2)s(-1) for the smallest GFH mesh size (100 x 140) to 64 x 10(-11) cm(2)s(-1) for the largest GFH mesh size (10 x 30). The rate-limiting process of intraparticle surface diffusion for arsenate adsorption by porous iron oxides appears analogous to organic compound adsorption by activated carbon despite differences in adsorption mechanisms (inner-sphere complexes for As versus hydrophobic interactions for organic contaminants). The findings are discussed in the context of intraparticle surface diffusion affecting packed-bed treatment system design and application of rapid small-scale column tests (RSSCTs) to simulate the performance of pilot- or full-scale systems at the bench-scale.