Building Environmental and Sociological Predictive Intelligence to Understand the Seasonal Threat of SARS-CoV-2 in Human Populations.

Current modeling practices for environmental and sociological modulated infectious diseases remain inadequate to forecast the risk of outbreak(s) in human populations, partly due to a lack of integration of disciplinary knowledge, limited availability of disease surveillance datasets, and overreliance on compartmental epidemiological modeling methods. Harvesting data knowledge from virus transmission (aerosols) and detection (wastewater) of SARS-CoV-2, a heuristic score-based environmental predictive intelligence system was developed that calculates the risk of COVID-19 in the human population. Seasonal validation of the algorithm was uniquely associated with wastewater surveillance of the virus, providing a lead time of 7-14 days before a county-level outbreak. Using county-scale disease prevalence data from the United States, the algorithm could predict COVID-19 risk with an overall accuracy ranging between 81% and 98%. Similarly, using wastewater surveillance data from Illinois and Maryland, the SARS-CoV-2 detection rate was greater than 80% for 75% of the locations during the same time the risk was predicted to be high. Results suggest the importance of a holistic approach across disciplinary boundaries that can potentially allow anticipatory decision-making policies of saving lives and maximizing the use of available capacity and resources.

Improved performance of nucleic acid-based assays for genetically diverse norovirus surveillance.

Nucleic acid-based assays, such as polymerase chain reaction (PCR), that amplify and detect organism-specific genome sequences are a standard method for infectious disease surveillance. However, challenges arise for virus surveillance because of their genetic diversity. Here, we calculated the variability of nucleotides within the genomes of 10 human viral species in silico and found that endemic viruses exhibit a high percentage of variable nucleotides (e.g., 51.4% for norovirus genogroup II). This genetic diversity led to the variable probability of detection of PCR assays (the proportion of viral sequences that contain the assay's target sequences divided by the total number of viral sequences). We then experimentally confirmed that the probability of the target sequence detection is indicative of the number of mismatches between PCR assays and norovirus genomes. Next, we developed a degenerate PCR assay that detects 97% of known norovirus genogroup II genome sequences and recognized norovirus in eight clinical samples. By contrast, previously developed assays with 31% and 16% probability of detection had 1.1 and 2.5 mismatches on average, respectively, which negatively impacted RNA quantification. In addition, the two PCR assays with a lower probability of detection also resulted in false negatives for wastewater-based epidemiology. Our findings suggest that the probability of detection serves as a simple metric for evaluating nucleic acid-based assays for genetically diverse virus surveillance.IMPORTANCENucleic acid-based assays, such as polymerase chain reaction (PCR), that amplify and detect organism-specific genome sequences are employed widely as a standard method for infectious disease surveillance. However, challenges arise for virus surveillance because of the rapid evolution and genetic variation of viruses. The study analyzed clinical and wastewater samples using multiple PCR assays and found significant performance variation among the PCR assays for genetically diverse norovirus surveillance. This finding suggests that some PCR assays may miss detecting certain virus strains, leading to a compromise in detection sensitivity. To address this issue, we propose a metric called the probability of detection, which can be simply calculated in silico using a code developed in this study, to evaluate nucleic acid-based assays for genetically diverse virus surveillance. This new approach can help improve the sensitivity and accuracy of virus detection, which is crucial for effective infectious disease surveillance and control.

Application of neighborhood-scale wastewater-based epidemiology in low COVID-19 incidence situations.

Wastewater-based epidemiology (WBE), an emerging approach for community-wide COVID-19 surveillance, was primarily characterized at large sewersheds such as wastewater treatment plants serving a large population. Although informed public health measures can be better implemented for a small population, WBE for neighborhood-scale sewersheds is less studied and not fully understood. This study applied WBE to seven neighborhood-scale sewersheds (average population of 1471) from January to November 2021. Community testing data showed an average of 0.004 % incidence rate in these sewersheds (97 % of monitoring periods reported two or fewer daily infections). In 92 % of sewage samples, SARS-CoV-2 N gene fragments were below the limit of quantification. We statistically determined 10-2.6 as the threshold of the SARS-CoV-2 N gene concentration normalized to pepper mild mottle virus (N/PMMOV) to alert high COVID-19 incidence rate in the studied sewershed. This threshold of N/PMMOV identified neighborhood-scale outbreaks (COVID-19 incidence rate higher than 0.2 %) with 82 % sensitivity and 51 % specificity. Importantly, neighborhood-scale WBE can discern local outbreaks that would not otherwise be identified by city-scale WBE. Our findings suggest that neighborhood-scale WBE is an effective community-wide disease surveillance tool when COVID-19 incidence is maintained at a low level.

Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics.

Monitoring the prevalence of SARS-CoV-2 variants is necessary to make informed public health decisions during the COVID-19 pandemic. PCR assays have received global attention, facilitating a rapid understanding of variant dynamics because they are more accessible and scalable than genome sequencing. However, as PCR assays target only a few mutations, their accuracy could be reduced when these mutations are not exclusive to the target variants. Here we introduce PRIMES, an algorithm that evaluates the sensitivity and specificity of SARS-CoV-2 variant-specific PCR assays across different geographical regions by incorporating sequences deposited in the GISAID database. Using PRIMES, we determined that the accuracy of several PCR assays decreased when applied beyond the geographic scope of the study in which the assays were developed. Subsequently, we used this tool to design Alpha and Delta variant-specific PCR assays for samples from Illinois, USA. In silico analysis using PRIMES determined the sensitivity/specificity to be 0.99/0.99 for the Alpha variant-specific PCR assay and 0.98/1.00 for the Delta variant-specific PCR assay in Illinois, respectively. We applied these two variant-specific PCR assays to six local sewage samples and determined the dominant SARS-CoV-2 variant of either the wild type, the Alpha variant, or the Delta variant. Using next-generation sequencing (NGS) of the spike (S) gene amplicons of the Delta variant-dominant samples, we found six mutations exclusive to the Delta variant (S:T19R, S:Δ156/157, S:L452R, S:T478K, S:P681R, and S:D950N). The consistency between the variant-specific PCR assays and the NGS results supports the applicability of PRIMES. IMPORTANCE Monitoring the introduction and prevalence of variants of concern (VOCs) and variants of interest (VOIs) in a community can help the local authorities make informed public health decisions. PCR assays can be designed to keep track of SARS-CoV-2 variants by measuring unique mutation markers that are exclusive to the target variants. However, the mutation markers may not be exclusive to the target variants because of regional and temporal differences in variant dynamics. We introduce PRIMES, an algorithm that enables the design of reliable PCR assays for variant detection. Because PCR is more accessible, scalable, and robust for sewage samples than sequencing technology, our findings will contribute to improving global SARS-CoV-2 variant surveillance.

Protective Effects of Gallic Acid Against NiSO4-Induced Toxicity Through Down-Regulation of the Ras/ERK Signaling Pathway in Beas-2B Cells.

BACKGROUND This study aimed to explore the preventive effects of gallic acid (GA) on the toxicity induced by NiSO4 in Beas-2B cells. MATERIAL AND METHODS Beas-2B cell viability was measured by MTT assay. The degree of oxidative stress was detected by measuring the levels of reactive oxygen species (ROS) and lipid peroxide (LPO). The rate of apoptosis was measured by flow cytometry. Ras/ERK-related protein levels were analyzed by Western blot analysis, which including Ras, ERK, c-Myc, PARP, and PARP cleavage. RESULTS MTT assay showed that NiSO4 induced cytotoxicity, while GA had a protective role against toxicity. Additionally, GA could reduce the apoptotic cell number and the level of ROS in Beas-2B cells induced by NiSO4. Western blot analysis demonstrated that NiSO4 could up-regulate the related protein in the Ras/ERK signaling pathway. Furthermore, we observed that GA could alleviate the toxicity of NiSO4 through regulating protein changes in the Ras/ERK signaling pathway. CONCLUSIONS Preventive effects of GA on NiSO4-induced cytotoxicity in Beas-2B cells may be through the Ras/ERK signaling pathways.

[Sediment and pore water nutrient characteristics in growing zones of Alternanthera philoxeroides in the Shiwuli River, Chaohu Lake].

In order to investigate the nitrogen and phosphorus characteristics of sediments and pore water in growing zones of aquatic macrophytes (Alternanthera philoxeroides), three classic representative sampling points in the planted Alternanthera philoxeroides fields (i. e. SP1, SP2 and SP3) and one reference site in the seldom vegetation (i. e. SP4) were chosen along the Shiwuli River, pouring into Chaohu Lake. Fifteen sediment cores were collected and sliced in-situ with a thickness of 2 cm, and a total of 80 samples were obtained. In the laboratory, both the contents of TN, TP, NH4(+) -N, NO3(-) -N, Fe/Al-P, Ca-P, organic matter in sediments and the concentrations of TN, TP, NH4(+) -N, NO3(-) -N and PO4(3-) -P in pore water were measured. And then, the vertical distribution profiles were illustrated and explored, and the correlations were also analyzed for the growing zones of Alternanthera philoxeroides. Through the comparison of profiles, it found that both nitrogen and phosphorus concentrations in pore water showed a rough similarity for three vegetation fields. At the surface sediment-overlying water interface, in general, there was a good agreement on the source-sink relationship for nitrogen and phosphorus corresponding to the SP1, SP2 and SP3. Study results showed that the vertical distribution of NH4(+) -N and NO3(-) -N in pore water within the depth of 0-18 cm could be characterized by using exponential functions such as Exp2PMod2 or Exp3P2 provided by OriginLab software, but PO4(3-) -P hardly ever did, implying that PO4(3-)-P might have a weaker regularity in solute diffusion than that of NH4(+) -N and NO3(-) -N.

[Distribution and bioavailability of nitrogen and phosphorus species in the urban dusts from Hefei City].

To find out the distribution and bioavailability of nitrogen (N) and phosphorus (P) species in the urban dusts of Hefei City, 52 samples were collected from impervious areas with six different urban land-use types. The contents of ammonia nitrogen (NH4(+) -N), nitrate nitrogen (NO3(-) -N), exchangeable P (Ex-P), Al-bound P (Al-P), Fe-bound P (Fe-P), occluded P (Oc-P), Ca-bound P (Ca-P), detrital apatite P (De-P), organic P (Or-P) as well as total nitrogen (TN) and total phosphorus (TP) were measured by sequential extraction methods. The studies on spatial distribution, correlation and bioavailability of nitrogen and phosphorus species were made according to the analyzed data. The results show that the TN is composed mainly of organic nitrogen (Or-N) while the TP consists chiefly of inorganic phosphorus (IP) in the urban dusts of Hefei City, and the spatial variability of nitrogen and phosphorus species contents are greatly affected by the mode of urban land-use type. In addition, there are significant correlations among partial nitrogen and phosphorus forms in dusts. Corresponding to different urban land-use types such as industrial area, commercial area, residential area, educational area, traffic area and public landscapes and city squares, the average ratios of bioavailable nitrogen content (the sum of NH4(+) -N and NO3(-) -N) to TN are 8.87%, 9.60%, 6.68%, 9.37%, 8.20% and 8.17%, respectively, while the mean ratios of bioavailable phosphorus content (the sum of Ex-P, Al-P and Fe-P) to TP, are equal to 6.70%, 18.19%, 10.10%, 9.69%, 10.64% and 14.03%, respectively.

[Distribution of metals in urban dusts of Hefei and health risk assessment].

This study focused on the characterization and the health risk assessment of heavy metals in the dust of Hefei City, China. Samples were collected from fifty two sampling points covering six land-use types. Most of the sites were impervious ground such as residential, commercial, industrial, educational and traffic areas, as well as public landscapes and city squares. Concentrations of Zn, Pb, Cu, Cd and Cr were measured to investigate their distribution and evaluate their risk to human health. The US EPA Health Risk Assessment Model was employed to evaluate the carcinogenic and non-carcinogenic risks of heavy metals to child and adult, respectively. The results showed that concentrations of Cd and Zn were 46 and 37 times higher than soil background values, respectively. The concentrations of Cu and Pb were 3-5 times, and Cr concentration was 1.5 times higher than the soil background values of Anhui Province. The carcinogenic risk indexes of Cr and Cd were 3.22 x 10(-7) and 2.26 x 10(-9), respectively, which were lower than the soil management standard of the US EPA, i.e. 1.0 x 10(-6). The total non-carcinogenic hazard index of the five metals for adults was only 0.212, but for children it reached to 1.259 and exceeded the safety threshold value (1.0), suggesting that the adverse health impact on children exposure to metals in urban dusts were relatively serious in Hefei. The ingestion of dust particles was the major exposure pathway for health risk. The orders of non-carcinogenic hazard indexes of land-use types and heavy metals were industrial area > public landscapes and city squares > commercial area > educational area > residential area > traffic area, and Pb > Cr > Zn > Cd > Cu, respectively.