Comparative analyses of SARS-CoV-2 RNA concentrations in Detroit wastewater quantified with CDC N1, N2, and SC2 assays reveal optimal target for predicting COVID-19 cases.

To monitor COVID-19 through wastewater surveillance, global researchers dedicated significant endeavors and resources to develop and implement diverse RT-qPCR or RT-ddPCR assays targeting different genes of SARS-CoV-2. Effective wastewater surveillance hinges on the appropriate selection of the most suitable assay, especially for resource-constrained regions where scant technical and socioeconomic resources restrict the options for testing with multiple assays. Further research is imperative to evaluate the existing assays through comprehensive comparative analyses. Such analyses are crucial for health agencies and wastewater surveillance practitioners in the selection of appropriate methods for monitoring COVID-19. In this study, untreated wastewater samples were collected weekly from the Detroit wastewater treatment plant, Michigan, USA, between January and December 2023. Polyethylene glycol precipitation (PEG) was applied to concentrate the samples followed by RNA extraction and RT-ddPCR. Three assays including N1, N2 (US CDC Real-Time Reverse Transcription PCR Panel for Detection of SARS-CoV-2), and SC2 assay (US CDC Influenza SARS-CoV-2 Multiplex Assay) were implemented to detect SARS-CoV-2 in wastewater. The limit of blank and limit of detection for the three assays were experimentally determined. SARS-CoV-2 RNA concentrations were evaluated and compared through three statistical approaches, including Pearson and Spearman's rank correlations, Dynamic Time Warping, and vector autoregressive models. N1 and N2 demonstrated the highest correlation and most similar time series patterns. Conversely, N2 and SC2 assay demonstrated the lowest correlation and least similar time series patterns. N2 was identified as the optimal target to predict COVID-19 cases. This study presents a rigorous effort in evaluating and comparing SARS-CoV-2 RNA concentrations quantified with N1, N2, and SC2 assays and their interrelations and correlations with clinical cases. This study provides valuable insights into identifying the optimal target for monitoring COVID-19 through wastewater surveillance.

Bioinformatics-based screening tool identifies a wide variety of human and zoonotic viruses in Trujillo-Peru wastewater.

Peru was one of the most affected countries during the COVID-19 pandemic. Moreover, multiple other viral diseases (enteric, respiratory, bloodborne, and vector-borne) are endemic and rising. According to Peru's Ministry of Health, various health facilities in the country were reallocated for the COVID-19 pandemic, thereby leading to reduced action to curb other diseases. Many viral diseases in the area are under-reported and not recognized. The One Health approach, in addition to clinical testing, incorporates environmental surveillance for detection of infectious disease outbreaks. The purpose of this work is to use a screening tool that is based on molecular methods, high throughput sequencing and bioinformatics analysis of wastewater samples to identify virus-related diseases circulating in Trujillo-Peru. To demonstrate the effectiveness of the tool, we collected nine untreated wastewater samples from the Covicorti wastewater utility in Trujillo-Peru on October 22, 2022. High throughput metagenomic sequencing followed by bioinformatic analysis was used to assess the viral diversity of the samples. Our results revealed the presence of sequences associated with multiple human and zoonotic viruses including Orthopoxvirus, Hepatovirus, Rhadinovirus, Parechovirus, Mamastrovirus, Enterovirus, Varicellovirus, Norovirus, Kobuvirus, Bocaparvovirus, Simplexvirus, Spumavirus, Orthohepevirus, Cardiovirus, Molliscipoxvirus, Salivirus, Parapoxvirus, Gammaretrovirus, Alphavirus, Lymphocryptovirus, Erythroparvovirus, Sapovirus, Cosavirus, Deltaretrovirus, Roseolovirus, Flavivirus, Betacoronavirus, Rubivirus, Lentivirus, Betapolyomavirus, Rotavirus, Hepacivirus, Alphacoronavirus, Mastadenovirus, Cytomegalovirus and Alphapapillomavirus. For confirmation purposes, we tested the samples for the presence of selective viruses belonging to the genera detected above. PCR based molecular methods confirmed the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), monkeypox virus (MPXV), noroviruses GI and GII (NoVGI and NoVGII), and rotavirus A (RoA) in our samples. Furthermore, publicly available clinical data for selected viruses confirm our findings. Wastewater or other environmental media surveillance, combined with bioinformatics methods, has the potential to serve as a systematic screening tool for the identification of human or zoonotic viruses that may cause disease. The results of this method can guide further clinical surveillance efforts and allocation of resources. Incorporation of this bioinformatic-based screening tool by public health officials in Peru and other Latin American countries will help manage endemic and emerging diseases that could save human lives and resources.

Tracking gene expression, metabolic profiles, and biochemical analysis in the halotolerant basidiomycetous yeast Rhodotorula mucilaginosa EXF-1630 during benzo[a]pyrene and phenanthrene biodegradation under hypersaline conditions.

Polyaromatic phenanthrene (Phe) and benzo[a]pyrene (BaP) are highly toxic, mutagenic, and carcinogenic contaminants widely dispersed in nature, including saline environments. Polyextremotolerant Rhodotorula mucilaginosa EXF-1630, isolated from Arctic sea ice, was grown on a huge concentration range -10 to 500 ppm- of Phe and BaP as sole carbon sources at hypersaline conditions (1 M NaCl). Selected polycyclic aromatic hydrocarbons (PAHs) supported growth as well as glucose, even at high PAH concentrations. Initially, up to 40% of Phe and BaP were adsorbed, followed by biodegradation, resulting in 80% removal in 10 days. While extracellular laccase, peroxidase, and un-specific peroxygenase activities were not detected, NADPH-cytochrome c reductase activity peaked at 4 days. The successful removal of PAHs and the absence of toxic metabolites were confirmed by toxicological tests on moss Physcomitrium patens, bacterium Aliivibrio fischeri, human erythrocytes, and pulmonary epithelial cells (A549). Metabolic profiles were determined at the midpoint of the biodegradation exponential phase, with added Phe and BaP (100 ppm) and 1 M NaCl. Different hydroxylated products were found in the culture medium, while the conjugative metabolite 1-phenanthryl-ß-D-glucopyranose was detected in the medium and in the cells. Transcriptome analysis resulted in 870 upregulated and 2,288 downregulated transcripts on PAHs, in comparison to glucose. Genomic mining of 61 available yeast genomes showed a widespread distribution of 31 xenobiotic degradation pathways in different yeast lineages. Two distributions with similar metabolic capacities included black yeasts and mainly members of the Sporidiobolaceae family (including EXF-1630), respectively. This is the first work describing a metabolic profile and transcriptomic analysis of PAH degradation by yeast.

Transcriptomic analysis of polyaromatic hydrocarbon degradation by the halophilic fungus Aspergillus sydowii at hypersaline conditions.

Polycyclic aromatic hydrocarbons (PAHs) are among the most persistent xenobiotic compounds, with high toxicity effects. Mycoremediation with halophilic Aspergillus sydowii was used for their removal from a hypersaline medium (1 M NaCl). A. sydowii metabolized PAHs as sole carbon sources, resulting in the removal of up to 90% for both PAHs [benzo [a] pyrene (BaP) and phenanthrene (Phe)] after 10 days. Elimination of Phe and BaP was almost exclusively due to biotransformation and not adsorption by dead mycelium and did not correlate with the activity of lignin modifying enzymes (LME). Transcriptomes of A. sydowii grown on PAHs, or on glucose as control, both at hypersaline conditions, revealed 170 upregulated and 76 downregulated genes. Upregulated genes were related to starvation, cell wall remodelling, degradation and metabolism of xenobiotics, DNA/RNA metabolism, energy generation, signalling and general stress responses. Changes of LME expression levels were not detected, while the chloroperoxidase gene, possibly related to detoxification processes in fungi, was strongly upregulated. We propose that two parallel metabolic pathways (mitochondrial and cytosolic) are involved in degradation and detoxification of PAHs in A. sydowii resulting in intracellular oxidation of PAHs. To the best of our knowledge, this is the most comprehensive transcriptomic analysis on fungal degradation of PAHs.

First demonstration that ascomycetous halophilic fungi (Aspergillus sydowii and Aspergillus destruens) are useful in xenobiotic mycoremediation under high salinity conditions.

Polycyclic aromatic hydrocarbons (PAH) and pharmaceutical compounds (PhC) are xenobiotics present in many saline wastewaters. Although fungi are known for their ability to remove xenobiotics, the potential of halophilic fungi to degrade highly persistent pollutants was not yet investigated. The use of two halophilic fungi, Aspergillus sydowii and Aspergillus destruens, for the elimination of PAH and PhC at saline conditions was studied. In saline synthetic medium both fungi used benzo-α-pyrene and phenanthrene as sole carbon source and removed over 90% of both PAH, A. sydowii due to biodegradation and A. destruens to bioadsorption. They removed 100% of a mixture of fifteen PAH in saline biorefinery wastewater. Test using Cucumis sativus demonstrated that wastewater treated with the two fungi lowered considerably the phytotoxicity. This study is the first demonstration that ascomycetous halophilic fungi, in contrast to other fungi (and in particular basidiomycetes) can be used for mycotreatments under salinity conditions.

Metabolic and inflammatory postprandial effect of a highly saturated fat meal and its relationship to abdominal obesity

Introduction: The postprandial stage is associated with the increase of markers related to cardiovascular risk, and its intensity depends on the metabolic state. Objective: To determine the impact of a high-fat meal intake on the metabolic and inflammatory profile, and its relationship to abdominal obesity. Materials and methods: This clinical trial included 42 individuals (21 with abdominal obesity). We measured glucose, insulin, lipid profile, reactive C protein, lipopolysaccharides, and interleukin 6 in fasting blood, and four hours after eating. Results: Besides obesity, we found insulin resistance and higher levels of fasting triacylglycerides and C-reactive protein. There were higher postprandial responses to glucose, insulin, and triacylglycerides. Interleukin 6 decreased in the non-obese group, and lipopolysaccharides increased in both groups. Conclusions: A saturated high-fat food intake produced a greater impact on the glycemic variables in the group with obesity, while it affected the lipids in both groups. However, the increase of triacylglycerides was higher in the presence of a high basal concentration, and it promoted the increase of lipopolysaccharides. The basal and postprandial inflammatory state affected the group with obesity more. The postprandial moment reflected the most frequent state of the individuals on a normal day and evidenced the capacity of the metabolic response to food intake, as well as early metabolic risk states.

Impacto metabólico e inflamatorio de una comida rica en grasas saturadas y su relación con la obesidad abdominal / Metabolic and inflammatory postprandial effect of a highly saturated fat meal and its relationship to abdominal obesity

Resumen Introducción. La etapa posprandial se asocia con el incremento de marcadores relacionados con el riesgo cardiovascular, cuya intensidad depende del estado metabólico. Objetivo. Determinar el impacto de la ingestión de una comida rica en grasas saturadas sobre el perfil metabólico e inflamatorio y su relación con la obesidad abdominal. Materiales y métodos. Se hizo un ensayo clínico en 42 individuos (21 con obesidad abdominal). Se midieron, en sangre, la glucosa, la insulina, el perfil lipídico, la proteína C reactiva, los lipopolisacáridos y la interleucina 6, en ayunas y después de la ingestión. Resultados. Además de la obesidad, se registró la presencia de resistencia a la insulina y de niveles elevados de triacilglicéridos y proteína C reactiva en ayunas. Asimismo, se detectaron niveles posprandiales más elevados de glucosa, insulina y triacilglicéridos. La interleucina 6 disminuyó en el grupo de personas sin obesidad y los lipopolisacáridos aumentaron en ambos grupos. Conclusión. La ingestión de una comida rica en grasas saturadas produjo un mayor impacto en las variables glucémicas en el grupo con obesidad y, aunque afectó de forma similar los lípidos en ambos grupos, el incremento de triacilglicéridos fue mayor en presencia de una concentración basal elevada y promovió el aumento de lipopolisacáridos. El estado inflamatorio basal y posprandial afectó en mayor medida al grupo con obesidad. El momento posprandial reflejó el estado más frecuente de los individuos en un día normal y permitió evidenciar la capacidad de respuesta metabólica frente a la ingestión de alimentos, así como los estados tempranos de riesgo metabólico.

Abstract Introduction: The postprandial stage is associated with the increase of markers related to cardiovascular risk, and its intensity depends on the metabolic state. Objective: To determine the impact of a high-fat meal intake on the metabolic and inflammatory profile, and its relationship to abdominal obesity. Materials and methods: This clinical trial included 42 individuals (21 with abdominal obesity). We measured glucose, insulin, lipid profile, reactive C protein, lipopolysaccharides, and interleukin 6 in fasting blood, and four hours after eating. Results: Besides obesity, we found insulin resistance and higher levels of fasting triacylglycerides and C-reactive protein. There were higher postprandial responses to glucose, insulin, and triacylglycerides. Interleukin 6 decreased in the non-obese group, and lipopolysaccharides increased in both groups. Conclusions: A saturated high-fat food intake produced a greater impact on the glycemic variables in the group with obesity, while it affected the lipids in both groups. However, the increase of triacylglycerides was higher in the presence of a high basal concentration, and it promoted the increase of lipopolysaccharides. The basal and postprandial inflammatory state affected the group with obesity more. The postprandial moment reflected the most frequent state of the individuals on a normal day and evidenced the capacity of the metabolic response to food intake, as well as early metabolic risk states.

Simple screening protocol for identification of potential mycoremediation tools for the elimination of polycyclic aromatic hydrocarbons and phenols from hyperalkalophile industrial effluents.

A number of fungal strains belonging to the ascomycota, basidiomycota and zygomycota genera were subjected to an in vitro screening regime to assess their ligninolytic activity potential, with a view to their potential use in mycoremediation-based strategies to remove phenolic compounds and polycyclic aromatic hydrocarbons (PAHs) from industrial wastewaters. All six basidiomycetes completely decolorized remazol brilliant blue R (RBBR), while also testing positive in both the guaiacol and gallic acid tests indicating good levels of lignolytic activity. All the fungi were capable of tolerating phenanthrene, benzo-α- pyrene, phenol and p-chlorophenol in agar medium at levels of 10 ppm. Six of the fungal strains, Pseudogymnoascus sp., Aspergillus caesiellus, Trametes hirsuta IBB 450, Phanerochate chrysosporium ATCC 787, Pleurotus ostreatus MTCC 1804 and Cadophora sp. produced both laccase and Mn peroxidase activity in the ranges of 200-560 U/L and 6-152 U/L, respectively, in liquid media under nitrogen limiting conditions. The levels of adsorption of the phenolic and PAHs were negligible with 99% biodegradation being observed in the case of benzo-α-pyrene, phenol and p-chlorophenol. The aforementioned six fungal strains were also found to be able to effectively treat highly alkaline industrial wastewater (pH 12.4). When this wastewater was supplemented with 0.1 mM glucose, all of the tested fungi, apart from A. caesiellus, displayed the capacity to remove both the phenolic and PAH compounds. Based on their biodegradative capacity we found T. hirsuta IBB 450 and Pseudogymnoascus sp., to have the greatest potential for further use in mycoremediation based strategies to treat wastestreams containing phenolics and PAHs.