RNA Concentration Research Articles

Development of Magnetic-Silica Particles and In-house Buffers Kit for SARS-CoV-2 and CDV RNA Extraction

Since the end of 2019, COVID-19 pandemic caused by the novel SARS-CoV-2 has become a serious problem for the world. Accurate and rapid techniques in testing and tracing are needed to control the virus spreading. Molecular diagnostics through gene amplification techniques, especially PCR, still become the gold standard for SARS-CoV-2 detection, which requires the first step of RNA extraction and purification. The limitations of commercial RNA extraction-purification kits during the pandemic caused a big problem in testing and tracing, especially for developing countries. A simple RNA extraction-purification kit based on magnetic-silica (MAGSi) beads and non-guanidine in-house buffers for RNA virus extraction-purification has been developed. Two types of MAGSi beads with different magnetic nanoparticles (MNPs) content were synthesized through a modified Stöber’s method using the sonication technique. The PCR result shows that both the MAGSi beads and the buffer can be used as a kit for RNA extraction-purification, tested for SARS-CoV-2 and Canine Distemper Virus. Further study shows that MAGSi-1 has better RNA extraction ability, and a higher concentration of RNA has been extracted. This is likely because of the smaller particle size distribution (50–1,500 nm distribution) and higher magnetization (20.2 emu/g) of MAGSi-1 compared to MAGSi-2 with 100–1,700 nm size distribution and 14.2 emu/g magnetization.

Results from the SARS-CoV-2 wastewater-based surveillance system in Denmark, July 2021 to June 2022

The microbiological analysis of wastewater samples is increasingly used for the surveillance of SARS-CoV-2 globally. We described the setup process of the national SARS-CoV-2 wastewater-based surveillance system in Denmark, presented its main results during the first year of activities, from July 2021 to June 2022, and discussed their operational significance. The Danish SARS-CoV-2 wastewater-based surveillance system was designed to cover 85 % of the population in Denmark and it entailed taking three weekly samples from 230 sites. Samples were RT-qPCR tested for SARS-CoV-2 RNA, targeting the genetic markers N1, N2 and RdRp, and for two faecal indicators, Pepper Mild Mottle Virus and crAssphage. We calculated the weekly SARS-CoV-2 RNA concentration in the wastewater from each sampling site and monitored it in view of the results from individual testing, at the national and regional levels. We attempted to use wastewater results to identify potential local outbreaks, and we sequenced positive wastewater samples using Nanopore sequencing to monitor the circulation of viral variants in Denmark. The system reached its full implementation by October 2021 and covered up to 86.4 % of the Danish population. The system allowed for monitoring of the national and regional trends of SARS-CoV-2 infections in Denmark. However, the system contribution to the identification of potential local outbreaks was limited by the extensive information available from clinical testing. The sequencing of wastewater samples identified relevant variants of concern, in line with results from sequencing of human samples. Amidst the COVID-19 pandemic, Denmark implemented a nationwide SARS-CoV-2 wastewater-based surveillance system that integrated routine surveillance from individual testing. Today, while testing for COVID-19 at the community level has been discontinued, the system is on the frontline to monitor the occurrence and spread of SARS-CoV-2 in Denmark.

Wastewater-based epidemiology for COVID-19 using dynamic artificial neural networks

Global efforts in vaccination have led to a decrease in COVID-19 mortality but a high circulation of SARS-CoV-2 is still observed in several countries, resulting in some cases of severe lockdowns. In this sense, wastewater-based epidemiology remains a powerful tool for supporting regional health administrations in assessing risk levels and acting accordingly. In this work, a dynamic artificial neural network (DANN) has been developed for predicting the number of COVID-19 hospitalized patients in hospitals in Valladolid (Spain). This model takes as inputs a wastewater epidemiology indicator for COVID-19 (concentration of RNA from SARS-CoV-2 N1 gene reported from Valladolid Wastewater Treatment Plant), vaccination coverage, and past data of hospitalizations. The model considered both the instantaneous values of these variables and their historical evolution. Two study periods were selected (from May 2021 until September 2022 and from September 2022 to July 2023). During the first period, accurate predictions of hospitalizations (with an overall range between 6 and 171) were favored by the correlation of this indicator with N1 concentrations in wastewater (r = 0.43, p < 0.05), showing accurate forecasting for 1 day ahead and 5 days ahead. The second period's retraining strategy maintained the overall accuracy of the model despite lower hospitalizations. Furthermore, risk levels were assigned to each 1 day ahead prediction during the first and second periods, showing agreement with the level measured and reported by regional health authorities in 95 % and 93 % of cases, respectively. These results evidenced the potential of this novel DANN model for predicting COVID-19 hospitalizations based on SARS-CoV-2 wastewater concentrations at a regional scale. The model architecture herein developed can support regional health authorities in COVID-19 risk management based on wastewater-based epidemiology.

A modeling pipeline to relate municipal wastewater surveillance and regional public health data

As COVID-19 becomes endemic, public health departments benefit from improved passive indicators, which are independent of voluntary testing data, to estimate the prevalence of COVID-19 in local communities. Quantification of SARS-CoV-2 RNA from wastewater has the potential to be a powerful passive indicator. However, connecting measured SARS-CoV-2 RNA to community prevalence is challenging due to the high noise typical of environmental samples. We have developed a generalized pipeline using in- and out-of-sample model selection to test the ability of different correction models to reduce the variance in wastewater measurements and applied it to data collected from treatment plants in the Chicago area. We built and compared a set of multi-linear regression models, which incorporate pepper mild mottle virus (PMMoV) as a population biomarker, Bovine coronavirus (BCoV) as a recovery control, and wastewater system flow rate into a corrected estimate for SARS-CoV-2 RNA concentration. For our data, models with BCoV performed better than those with PMMoV, but the pipeline should be used to reevaluate any new data set as the sources of variance may change across locations, lab methods, and disease states. Using our best-fit model, we investigated the utility of RNA measurements in wastewater as a leading indicator of COVID-19 trends. We did this in a rolling manner for corrected wastewater data and for other prevalence indicators and statistically compared the temporal relationship between new increases in the wastewater data and those in other prevalence indicators. We found that wastewater trends often lead other COVID-19 indicators in predicting new surges.

Non-Small Cell Lung Cancer Testing on Reference Specimens: An Italian Multicenter Experience.

Biomarker testing is mandatory for the clinical management of patients with advanced non-small cell lung cancer (NSCLC). Myriads of technical platforms are now available for biomarker analysis with differences in terms of multiplexing capability, analytical sensitivity, and turnaround time (TAT). We evaluated the technical performance of the diagnostic workflows of 24 representative Italian institutions performing molecular tests on a series of artificial reference specimens built to mimic routine diagnostic samples. Sample sets of eight slides from cell blocks of artificial reference specimens harboring exon19 EGFR (epidermal growth factor receptor) p.E746_AT50del, exon2 KRAS (Kirsten rat sarcoma viral oncogene homologue) p.G12C, ROS1 (c-ros oncogene1)-unknown gene fusion, and MET (MET proto-oncogene, receptor tyrosine kinase) Δ exon14 skipping were distributed to each participating institution. Two independent cell block specimens were validated by the University of Naples FedericoII before shipment. Methodological and molecular data from reference specimens were annotated. Overall, a median DNA concentration of 3.3ng/µL (range 0.1-10.0ng/µL) and 13.4ng/µL (range 2.0-45.8ng/µL) were obtained with automated and manual technical procedures, respectively. RNA concentrations of 5.7ng/µL (range 0.2-11.9ng/µL) and 9.3ng/µL (range 0.5-18.0ng/µL) were also detected. KRAS exon2 p.G12C, EGFR exon19 p.E736_A750del hotspot mutations, and ROS1 aberrant transcripts were identified in all tested cases, whereas 15 out of 16 (93.7%) centers detected MET exon14 skipping mutation. Optimized technical workflows are crucial in the decision-making strategy of patients with NSCLC. Artificial reference specimens enable optimization of diagnostic workflows for predictive molecular analysis in routine clinical practice.

Monitoring Real-Time Temperature Dynamics of a Short RNA Hairpin Using Förster Resonance Energy Transfer and Circular Dichroism.

RNA molecules play crucial roles in gene expression regulation and cellular signaling, and these functions are governed by the formation of RNA secondary and tertiary structures. These structures are highly dynamic and subject to rapid changes in response to environmental cues, temperature in particular. Thermosensitive RNA secondary structures have been harnessed by multiple organisms to survey their temperature environment and to adjust gene expression accordingly. It is thus highly desirable to observe RNA structural changes in real time over a range of temperatures. Multiple approaches have been developed to study structural dynamics, but many of these require extensive processing of the RNA, large amounts of RNA input, and/or cannot be applied under physiological conditions. Here, we describe the use of a dually fluorescently labeled RNA oligonucleotide (containing a predicted hairpin structure) to monitor subtle RNA structural dynamics in vitro by Förster resonance energy transfer (FRET) and circular dichroism (CD) spectroscopy. These approaches can be employed under physiologically relevant conditions over a range of temperatures and with RNA concentrations as low as 200nM; they enable us to observe RNA structural dynamics in real time and to correlate these dynamics with changes in biological processes such as translation.

MiRNA profiling in the aqueous humour in patients with Fuch's endothelial corneal dystrophy

Aims: The aim of the study was to determine and compare the expression profiles of miRNA molecules in the aqueous humour (AH) of patients with Fuch's endothelial corneal dystrophy (FECD) and patients with normal corneal endothelium undergoing cataract surgery.Methods: The study consisted of 20 Caucasian patients (10 FECD and 10 control patients) who underwent comprehensive ophthalmology examination, thus routine corneal transplant or cataract surgery. 100 μL of AH were obtained from the anterior chamber at the beginning of the surgery with special care to avoid contamination with blood tears. The total RNA was isolated from the AH samples using an miRNeasy Serum/Plasma kit according to the manufacturer's instructions. The RNA concentration was determined by using NanoDrop2000c spectrophotometer. In addition, RNA analysis was performed using Agilent Bioanalyzer2100 and PicoRNA Kit according to the manufacturer's protocol. A microarray system (GeneChip miRNA 4.0 Array chip, Affymetrix) was used to determine the miRNA expression profiles. The RNA preparation and hybridization were performed according to the manufacturer's protocol, with one modification to extend the hybridization time to 42 h. The gene chips were scanned with an Affymetrix GeneChip Scanner 3000.Results: We found significant overexpression of hsa‐miR‐4532, hsa‐miR‐6800‐5p, hsa‐miR‐3621, hsa‐miR‐4270, hsa‐miR‐548ac, hsa‐miR‐328‐5p, hsa‐miR‐6771 ‐5p, hsa‐miR‐6858‐5p, hsa‐miR‐548a‐3p, hsa‐miR‐6069, hsa‐miR‐6716‐5p, hsa‐miR‐7151‐3p, hsa‐miR‐5189‐5p, hsa ‐miR‐4279, hsa‐miR‐1233‐5p, hsa‐miR‐455‐3p in patients with FECD compared to those patients with normal corneal endothelium. Reduced expression of hsa‐miR‐3613‐3p, hsa‐miR‐1298‐3p, hsa‐miR‐16‐2‐3p, hsa‐miR‐4668‐5p was observed in patients with FECD in addition to the control group.Conclusions: The analysis of miRNA expression profiles and their application as potential biomarkers will facilitate and accelerate the diagnosis of FECD, as well as enable the development of individualized molecularly targeted therapy.

Bioactive additives from the dorsal dermis of mice for enhanced vascularization in 3D bioprinting.

Effective angiogenesis is essential for creating complex vascular networks in tissue engineering; however, there is a scarcity of safe and potent pro-angiogenic factors. Although a decellularized extracellular matrix (dECM) offers excellent biocompatibility and is widely used in tissue engineering as a pro-angiogenic additive, its conventional extraction technique resulting in significant loss of bioactivity limits clinical potential. The dorsal dermal tissue has rich blood perfusion and its dECM is rich in angiogenic factors. In this study, the dECM components from the dorsal dermis of mice (DD) were produced to enhance in vitro and in vivo pro-angiogenic abilities using a novel physical method. Morphological studies showed no significant difference between DD-wild-type (DD-wt) and DD-wild-type-newborn (DD-wtn), and there was also no difference in DNA or RNA concentration. In addition, DD-wtn outperformed DD-wt in maintaining the stemness of MSCs, promoting inflammatory response and facilitating endothelial cell differentiation. It is of greater significance to note that the dermal combined fibrous capsule thickness is greater in the DD-wt treated group than in the DD-wtn group. Furthermore, the number of blood vessels in the subcutaneously implanted scaffold with DD-wtn increased by 233%. Consequently, our current finding provides a promising strategy to produce a novel pro-angiogenic bioink additive for enhancing vascularization in 3D bioprinting.

Evaluation of short-term hair follicle storage conditions for maintenance of RNA integrity.

Hair follicles provide an easily accessible tissue for interrogating gene expression for multiple purposes in mammals. RNAlater® is a liquid storage solution that stabilises and preserves cellular RNA, eliminating the need to immediately process or freeze tissue specimens. The manufacturer advises storage of samples at 2-8°C overnight before transfer to -20°C. This study aimed to evaluate RNA integrity in hair follicle samples collected from horses, stabilized in RNAlater®, and stored under three short-term storage conditions. Mane hair samples complete with follicles were collected from four horses at a single time point. Approximately 15 hairs were placed in each of three 2 mL tubes containing 0.75ml RNAlater® solution. Test group A was stored at 4°C for 24-h, then decanted and stored at -20°C. Test groups B and C were stored at 4°C and 19°C (room temperature) respectively for 7 days, then decanted and stored at -20°C. RNA was isolated from all samples and RNA quantity and quality were measured. One-way ANOVA revealed no difference in RNA concentration (A:516 +/-125 ng/ml, B:273+/-93 ng/ml, C:476+/-176 ng/ml;P = 0.2) or quality (A:9.5 +/-0.19, B:9.8+/-0.09, C:9.2+/-0.35 RIN; P = 0.46) between the test groups. There were no group differences in mean Cycle Threshold values from qPCR validation assays confirming high-quality template cDNA. The results suggest that storage of hair follicles for one week in RNAlater® at cool or room temperature conditions will not compromise RNA integrity and will permit extended transport times from remote sampling locations without the need for freezing.

RNP granules in ALS and neurodegeneration: From multifunctional membraneless organelles to therapeutic opportunities.

Amyotrophic lateral sclerosis (ALS) and related neurodegenerative diseases are characterised by dysfunction of a host of RNA-binding proteins (RBPs) and a severely disrupted RNA metabolism. Recently, RBP-harbouring phase-separated complexes, ribonucleoprotein (RNP) granules, have come into the limelight as "crucibles" of neuronal pathology in ALS. RNP granules are indispensable for the multitude of regulatory processes underlying cellular RNA metabolism and serve as critical organisers of cellular biochemistry. Neurons, highly specialised cells, heavily rely on RNP granules for efficient trafficking, signalling and stress responses. Multiple RNP granule components, primarily RBPs such as TDP-43 and FUS, are affected by ALS mutations. However, even in the absence of mutations, RBP proteinopathies represent pathophysiological hallmarks of ALS. Given the high local concentrations of RBPs and RNAs, their weakened or enhanced interactions within RNP granules disrupt their homeostasis. Thus, the physiological process of phase separation and RNP granule formation, vital for maintaining the high-functioning state of neuronal cells, becomes their Achilles heel. Here, we will review the recent literature on the causes and consequences of abnormal RNP granule functioning in ALS and related disorders. In particular, we will summarise the evidence for the network-level dysfunction of RNP granules in these conditions and discuss considerations for therapeutic interventions to target RBPs, RNP granules and their network as a whole.

Parity affects mammary development in late-pregnant swine.

The goal of this project was to determine whether various measures of mammary development differed between gilts and multiparous sows at the end of gestation. During gestation, Yorkshire × Landrace gilts (n = 19) and sows (second and third gestations, n = 17) were fed one daily meal of a conventional corn-based diet, where the amount fed was based on body weight (BW) and backfat thickness (BF) at mating. On day 110 ± 1 of gestation, a jugular blood sample was obtained from all gilts and sows to measure insulin-like growth factor-1 (IGF-1), glucose, free fatty acids, and urea. On that same day, BW and BF were measured and animals were euthanized. Mammary glands from one side of the udder were dissected for compositional analyses. The fifth gland of the contralateral row of mammary glands was sampled for histology and immunohistochemical localization of Ki67. There was less total parenchyma (1,437.4 vs. 2,004.7 ± 127.1g; P < 0.001) and total extraparenchymal tissue (1,691.0 vs. 2,407.0 ± 125.3g; P < 0.001) in mammary glands of gilts compared to those from sows. When these values were expressed per kg BW (226.0 and 284.0 ± 2.7kg for gilts and sows, respectively), parenchymal mass did not differ (P > 0.10), while extraparenchymal tissue weight tended to be less in gilts than sows (P = 0.07). All components within the parenchyma differed by parity (P < 0.001). Specifically, parenchymal tissue from gilts contained a greater proportion of fat and dry matter (DM), a lower proportion of protein, and lower concentrations of DNA (6.59 vs. 9.35 ± 0.53mg/g DM) and RNA (7.76 vs. 12.33 ± 0.70mg/g DM) than that from sows. On the other hand, the circumference of alveolar lumens was greater in gilts than sows (P < 0.001), while the percentage of epithelial cells that were positive for Ki67, a marker of cell proliferation, was greater in sows than gilts (P < 0.05). Circulating concentrations of IGF-1 were greater in gilts than in multiparous sows (45.0 vs. 27.3 ± 2.8ng/mL, P < 0.001). None of the other blood variables were changed by parity. Results show a marked effect of parity on mammary gland development in swine. At the end of gestation, the mammary glands of gilts had less parenchyma with lower epithelial proliferation than glands from multiparous sows. These differences could alter the response of mammary tissue to various nutritional or endocrine signals. This information is crucial for the development of management strategies designed to maximize sow milk yield.

Fine-tuning RNA extraction protocols for polysaccharide-rich freshwater red algae (Rhodophyta).

Freshwater red algae are important primary producers, widely distributed, contributing significantly to nutrient cycling in aquatic ecosystems. Recent studies have focused on identifying the effect of different environmental conditions such as light on the gene expression in photosynthesis pathways. However, obtaining the necessary RNA quantity and quality for sequencing from these algae has been challenging. Although RNA extractions have been optimized for model organisms, RNA extraction for non-model organisms, such as gelatinous (polysaccharide-rich) red algae, requires considerable troubleshooting. The common freshwater red alga, Batrachospermum gelatinosum , was used to test protocols. The extraction efficiency of various sample disruption methods in combination with seven RNA extraction kits was compared. Using a 2-minute disruption procedure with a modification of TRIzol ™ Plus RNA Purification Kit (PureLink ™ RNA Mini Kit + Trizol ™ ) protocol resulted in significantly higher RIN scores (p < 0.05) and high RNA concentration, compared to other methods. The fine-tuned protocol yielded quality RNA (RIN>7) in high concentrations for subsequent sequencing.

DNA-directed formation of plasmonic core-satellite nanostructures for quantification of hepatitis C viral RNA.

Hepatitis C virus (HCV) continues to be a significant public health challenge, affecting an estimated 71 million people globally and posing risks of severe liver diseases. Despite advancements in treatments, diagnostic limitations hinder the global elimination efforts targeted by 2030. This study introduces an innovative diagnostic approach, integrating catalytic hairpin assembly (CHA) with plasmonic core-satellite gold nanoparticle (AuNP) assemblies, to enable sensitive and specific detection of HCV RNA. We optimized the stoichiometry of DNA hairpins to form highly stable three-way junctions (3WJs), minimizing non-specific reactions in an enzyme-free, isothermal amplification process. The resulting dual-transduction biosensor combines colorimetric and surface-enhanced Raman spectroscopy (SERS) techniques, utilizing the Raman reporter malachite green isothiocyanate (MGITC) for signal generation. Our system targets a conserved 23-nucleotide sequence within the HCV 5'-UTR, essential for RNA replication, facilitating pan-genotypic HCV detection that complements direct-acting antiviral strategies. We evaluated the biosensor's efficacy using fluorescence spectroscopy, native PAGE, AFM, and TEM. Findings indicate that the 60 nm core AuNPs surrounded by 20 nm satellite AuNPs achieved a ten-fold increase in sensitivity over the 10 nm satellites, detecting HCV RNA concentrations as low as 1.706 fM. This sensitivity is crucial, given the extremely low viral loads present during early infection stages. Our research demonstrates the promise of enzyme-free molecular biosensors for HCV, with the potential to provide cost-efficient, rapid, point-of-care testing, although further sensitivity enhancements are needed to address the challenges of early-stage detection.

Comparação de sete differentes RT-qPCR para detecção do virus da febre aftosa

Abstract The prompt and accurate diagnosis of foot-and-mouth disease outbreaks is crucial to curb the swift transmission of its causative agent, the foot-and-mouth disease virus (FMDV), which poses a substantial threat to the nation’s livestock. This study aimed to perform a comparative analysis of various RT-qPCR methods for the detection of FMDV. The methods evaluated for the 3D region demonstrated similar sensitivity and specificity. Nevertheless, noticeable distinctions emerged in samples with low RNA concentration. While these methods can be interchangeably utilized with consistent outcomes when handling a large number of samples sent to the laboratory to pinpoint an outbreak, minor variations may assume significance when working with a limited quantity of samples containing low FMDV RNA copies.

Development of an Automatic PCR System Combined with Magnetic Bead-based Viral RNA Concentration and Extraction

Development of an Automatic PCR System Combined with Magnetic Bead-based Viral RNA Concentration and Extraction

Universal nucleic acid donor screening revealed epidemiological features of hepatitis E and prevented transfusion-transmitted infection in Japan.

More than 45 cases of transfusion-transmitted hepatitis E virus infection (TT-HEV) have been reported in Japan. Therefore, in 2020, universal individual donation nucleic acid amplification testing (ID-NAT) was implemented for HEV. We characterized HEV NAT-positive blood donors. The number of new HEV infections and the asymptomatic infection rate were estimated using the HEV NAT-positive rate. HEV RNA quantitation, phylogenetic analysis, and antibody tests were performed, and the residual risk of TT-HEV was assessed based on the lookback study results. A total of 5,075,100 blood donations were screened with ID-NAT during the first year of implementation, among which 2804 (0.055%; males: 0.060%, females: 0.043%) were NAT-positive with regional differences. Approximately 270,000 new HEV infection cases were estimated to occur annually in Japan, with an asymptomatic infection rate of 99.9%. The median HEV RNA concentration, excluding cases below the limit of quantification, was 205 IU/mL. Among the 1113 cases where the genotype could be determined, HEV-3 and HEV-4 accounted for 98.8% (1100) and 1.2% (13), respectively. The maximum duration of HEV viremia, including the pre- and post-ID-NAT window periods, was estimated to be 88.2 days. Within the 3 years since ID-NAT implementation, no confirmed cases of breakthrough TT-HEV were observed. Multiple indigenous HEV strains are prevalent in Japan, infecting a significant number of individuals. However, since the implementation of ID-NAT, TT-HEV has been prevented due to the test's high sensitivity.

Investigation of oncolytic potential of vaccine strains of yellow fever and tick-borne encephalitis viruses against glioblastoma and pancreatic carcinoma cell lines

Flaviviruses, possessing natural neurotropicity could be used in glioblastoma therapy using attenuated strains or as a delivery system for antitumor agents in an inactivated form. To investigate the sensitivity of glioblastoma and pancreatic carcinoma cell lines to vaccine strains of yellow fever and tick-borne encephalitis viruses. Cell lines: glioblastoma GL-6, T98G, LN-229, pancreatic carcinoma MIA RaCa-2 and human pancreatic ductal carcinoma PANC-1. Viral strains: 17D yellow fever virus (YF), Sofjin tick-borne encephalitis virus (TBEV). Virus concentration were determined by plaque assay and quantitative PCR. Determination of cell sensitivity to viruses by MTT assay. 17D YF was effective only against pancreatic carcinoma tumor cells MIA Paca-2 and had a limited effect against PANC-1. In glioblastoma cell lines (LN229, GL6, T98G), virus had no oncolytic effect and the viral RNA concentration fell in the culture medium. Sofjin TBEV showed CPE50 against MIA Paca-2 and a very limited cytotoxic effect against PANC-1. However, it had no oncolytic effect against glioblastoma cell lines (LN229, T98G and GL6), although virus reproduction continued in these cultures. For the GL6 glioblastoma cell line, the viral RNA concentration at the level with the infection dose was determined within 13 days, despite medium replacement, while in the case of the LN229 cell line, the virus concentration increased from 1 × 109 to 1 × 1010 copies/ml. Tumor behavior in organism is more complex and is determined by different microenvironmental factors and immune status. In the future, it is advisable to continue studying the antitumor oncolytic and immunomodulatory effects of viral strains 17D YF and Sofjin TBEV using in vivo models.

Detection of enteroviruses related to hand foot and mouth disease in wastewater of Asian communities

Hand, foot, and mouth disease (HFMD) is contagious and predominantly affects children below the age of five. HFMD-associated serotypes of Enterovirus A (EVA) family include EVA71, Coxsackievirus A type 6 (CVA6), 10 (CVA10), and 16 (CVA16). Although prevalent in numerous Asian countries, studies on HFMD-causing agents in wastewater are scarce. This study aimed to conduct wastewater surveillance in various Asian communities to detect and quantify serotypes of EVA associated with HFMD. In total, 77 wastewater samples were collected from Indonesia, the Philippines, Thailand, and Vietnam from March 2022 to February 2023. The detection ratio for CVA6 RNA in samples from Vietnam was 40 % (8/20). The detection ratio for CVA6 and EVA71 RNA each was 25 % (5/20) for the Indonesian samples, indicating the need for clinical surveillance of CVA6, as clinical reports have been limited. For the Philippines, 12 % (2/17) of the samples were positive for CVA6 and EVA71 RNA each, with only one quantifiable sample each. Samples from Thailand had a lower detection ratio (1/20) for CVA6 RNA, and the concentration was unquantifiable. Conversely, CVA10 and CVA16 RNAs were not detected in any of the samples. The minimum and maximum concentrations of CVA6 RNA were 2.7 and 3.9 log10 copies/L and those for EVA71 RNA were 2.5 and 4.9 log10 copies/L, respectively. This study underscores the importance of wastewater surveillance in understanding the epidemiology of HFMD-associated EVA serotypes in Asian communities. Long-term wastewater surveillance is recommended to monitor changes in dominant serotypes, understand seasonality, and develop effective prevention and control strategies for HFMD.

Wastewater-based surveillance as a tool for public health action: SARS-CoV-2 and beyond.

Wastewater-based surveillance (WBS) has undergone dramatic advancement in the context of the coronavirus disease 2019 (COVID-19) pandemic. The power and potential of this platform technology were rapidly realized when it became evident that not only did WBS-measured SARS-CoV-2 RNA correlate strongly with COVID-19 clinical disease within monitored populations but also, in fact, it functioned as a leading indicator. Teams from across the globe rapidly innovated novel approaches by which wastewater could be collected from diverse sewersheds ranging from wastewater treatment plants (enabling community-level surveillance) to more granular locations including individual neighborhoods and high-risk buildings such as long-term care facilities (LTCF). Efficient processes enabled SARS-CoV-2 RNA extraction and concentration from the highly dilute wastewater matrix. Molecular and genomic tools to identify, quantify, and characterize SARS-CoV-2 and its various variants were adapted from clinical programs and applied to these mixed environmental systems. Novel data-sharing tools allowed this information to be mobilized and made immediately available to public health and government decision-makers and even the public, enabling evidence-informed decision-making based on local disease dynamics. WBS has since been recognized as a tool of transformative potential, providing near-real-time cost-effective, objective, comprehensive, and inclusive data on the changing prevalence of measured analytes across space and time in populations. However, as a consequence of rapid innovation from hundreds of teams simultaneously, tremendous heterogeneity currently exists in the SARS-CoV-2 WBS literature. This manuscript provides a state-of-the-art review of WBS as established with SARS-CoV-2 and details the current work underway expanding its scope to other infectious disease targets.

Estimation of Norovirus infections in Japan: An application of wastewater-based epidemiology for enteric disease assessment

Noroviruses of genogroup I (NoV GI) and NoV GII are the primary causes of acute gastroenteritis (AGE) in developed countries. However, asymptomatic and untested NoV infections lead to an underestimation of AGE cases, and the lack of mandatory viral identification in clinical cases hinders precise estimation of NoV infections. Back estimation of NoV infections in the community using a wastewater-based epidemiology (WBE) approach can provide valuable insights into the disease's extent, progression, and epidemiology, aiding in developing effective control strategies. This study employed a one-step reverse transcription-quantitative PCR to quantify NoVs GI and GII in wastewater samples (n = 83) collected twice a week from June 2022 to March 2023 in Japan. All samples from the Winter-Spring (n = 27) tested positive for NoV GI and GII RNA, while 73 % and 88 % of samples from the Summer-Autumn (n = 56) were positive for NoV GI and NoV GII RNA, respectively. Significantly higher concentrations of NoV GI/GII RNA were found in the Winter-Spring season compared to the Summer-Autumn season. NoV RNA was consistently detected in wastewater throughout the year, demonstrating the persistence of AGE cases in the catchment, suggesting an endemic NoV infection. Estimates of NoV infection incorporated viral RNA concentrations, wastewater parameters, and signal persistence in a mass balance equation using Monte Carlo Simulation. The median estimated NoV GI infections per 100,000 population for Summer-Autumn was 133 and for the Winter-Spring season, it was 881. Estimated NoV GII infections were 1357 for Summer-Autumn and 11,997 for the Winter-Spring season per 100,000 population. The estimated NoV infections exceeded by 3.2 and 23.9 folds than the reported AGE cases in Summer-Autumn and Winter-Spring seasons, respectively. The seasonal trend of estimated NoV infections closely matched that of AGE cases, highlighting the utility of WBE in understanding the epidemiology of enteric infections.