Detection of SARS-CoV-2 Genome in Stool and Plasma Samples of Laboratory Confirmed Iranian COVID-19 Patients

LAMP-CRISPR/Cas12a-based impedimetric biosensor powered by Fe3O4@Au-(S-polyA-S)-Au for detection of SARS-CoV-2

A low-cost, lab-made polytetrafluoroethylene micro-cell, equipped with three electrodes, wasd eveloped for the impedimetric detection of SARS-CoV-2. The gold working electrode was modified with a double-ended thiolated poly-adenine probe, which was conjugated with magnetic Fe₃O₄@Au nanoparticles (Fe3O4@Au-(S-polyA-S)-Au). After the loop-mediated isothermal amplification (LAMP) of viral RNA, the single-guide RNA (sgRNA), specifically bound to the SARS-CoV-2 target sequence, activates Cas12a. Cas12a then cleaved the immobilized probe. As a result, the magnetic Fe3O4@Au nanoparticles were released and adsorbed onto the gold electrode surface, using an external magnet. This process increased the physical surface area of the gold electrode, facilitating redox ion ([FeIII/II(CN)6]3-/4-) electron transfer. The decrease in the charge transfer resistance was utilized for SARS-CoV-2 detection. Our LAMP-CRISPR/Cas12a-based impedimetric biosensor, powered by Fe3O4@Au-(S-polyA-S)-Au, demonstrated impressive capabilities, including a remarkable detection limit of 0.8 aM (0.48 copies/µL) and a linear range of 0.01 to 36.06 fM.

Wastewater surveillance of severe acute respiratory syndrome coronavirus-2 in open drains of two Indian megacities captures evolutionary lineage transitions: a zonation approach

Wastewater-based environmental surveillance (WBES) has been proven as proxy tool for monitoring nucleic acids of pathogens shed by infected population before clinical outcomes. The poor sewershed network of low to middle-income countries (LMICs) leads to most of the wastewater flow through open drains. We studied the effectiveness of WBES using open drain samples to monitor the emergence of the SARS-CoV-2 variants in 2 megacities of India having dense population through zonation approach. Samples from 28 locations spanned into 5 zones of Pune region, Maharashtra, India, were collected on a weekly basis during October 2021 to July 2022. Out of 1115 total processed samples, 303 (~ 27%) tested positive for SARS-CoV-2. The periodical rise and fall in the percentage positivity of the samples was found to be in sync with the abundance of SARS-CoV-2 RNA and the reported COVID-19 active cases for Pune city. Sequencing of the RNA obtained from wastewater samples confirmed the presence of SARS-CoV-2. Of 337 sequences, lineage identification for 242 samples revealed 265 distinct SARS-CoV-2 variants including 10 highly transmissible ones. Importantly, transition from Delta to Omicron variant could be detected in wastewater samples 2 weeks prior to any clinically reported Omicron cases in India. Thus, this study demonstrates the usefulness of open drain samples for real-time monitoring of a viral pathogen's evolutionary dynamics and could be implemented in LMICs.

Prevalence of SARS-CoV-2 virus in saliva, stool, and urine samples of COVID-19 patients in Bihar, India

Introduction. The coronavirus illness caused by SARS-CoV-2 can cause multiple organ involvement, with varying degrees of severity. Besides inhalation as a route for transmission, feco-oral has also been proposed. Its transmission to sewage systems is a growing public health issue. Objective. To detect SARS-CoV-2 RNA in non-respiratory samples (saliva, urine, and stool) collected from COVID-19 cases, in Bihar. Methods. This cross-sectional observational study was conducted from January 2021 to March 2022 on human non-respiratory samples. A total of 345 samples including saliva (116), stool (97), and urine (132) were collected from 143 COVID-19 cases. Samples were analysed for SARS-CoV-2 by multiplex RT-PCR targeted against E, ORF 1ab, and RdRp genes. Results. In this study, out of 143 cases, a total of 107 (74.8 %) were positive for SARS-CoV-2 RNA in at least one of the non-respiratory samples. Conclusion. There is a high prevalence of SARS-CoV-2 virus in non-respiratory samples.

Long non-coding RNAs ANRIL, THRIL, and NEAT1 as potential circulating biomarkers of SARS-CoV-2 infection and disease severity

The current outbreak of coronavirus disease 2019 (COVID-19) is a global emergency, as its rapid spread and high mortality rate, which poses a significant threat to public health. Innate immunity plays a crucial role in the primary defense against infections, and recent studies have highlighted the pivotal regulatory function of long non-coding RNAs (lncRNAs) in innate immune responses. This study aims to assess the circulating levels of lncRNAs namely ANRIL, THRIL, NEAT1, and MALAT1 in the blood of moderate and severe SARS-CoV-2 infected patients, in comparison to healthy individuals. Additionally, it aims to explore the potential of these lncRNAs as biomarkers for determining the severity of the disease. The blood samples were collected from a total of 38 moderate and 25 severe COVID-19 patients, along with 30 healthy controls. The total RNA was extracted and qPCR was performed to evaluate the blood levels of the lncRNAs. The results indicate significantly higher expression levels of lncRNAs ANRIL and THRIL in severe patients when compared to moderate patients (P value = 0.0307, P value = 0.0059, respectively). Moreover, the expression levels of lncRNAs ANRIL and THRIL were significantly up-regulated in both moderate and severe patients in comparison to the control group (P value < 0.001, P value < 0.001, P value = 0.001, P value < 0.001, respectively). The expression levels of lncRNA NEAT1 were found to be significantly higher in both moderate and severe COVID-19 patients compared to the healthy group (P value < 0.001, P value < 0.001, respectively), and there was no significant difference in the expression levels of NEAT1 between moderate and severe patients (P value = 0.6979). The expression levels of MALAT1 in moderate and severe patients did not exhibit a significant difference compared to the control group (P value = 0.677, P value = 0.764, respectively). Furthermore, the discriminative power of ANRIL and THRIL was significantly higher in the severe patient group than the moderate group (Area under curve (AUC) = 0.6879; P-value = 0.0122, AUC = 0.6947; P-value = 0.0093, respectively). In conclusion, the expression levels of the lncRNAs ANRIL and THRIL are correlated with the severity of COVID-19 and can be regarded as circulating biomarkers for disease progression.

Technologies for pollutant removal and resource recovery from blackwater: a review

Blackwater (BW), consisting of feces, urine, flushing water and toilet paper, makes up an important portion of domestic wastewater. The improper disposal of BW may lead to environmental pollution and disease transmission, threatening the sustainable development of the world. Rich in nutrients and organic matter, BW could be treated for resource recovery and reuse through various approaches. Aimed at providing guidance for the future development of BW treatment and resource recovery, this paper presented a literature review of BWs produced in different countries and types of toilets, including their physiochemical characteristics, and current treatment and resource recovery strategies. The degradation and utilization of carbon (C), nitrogen (N) and phosphorus (P) within BW are underlined. The performance of different systems was classified and summarized. Among all the treating systems, biological and ecological systems have been long and widely applied for BW treatment, showing their universality and operability in nutrients and energy recovery, but they are either slow or ineffective in removal of some refractory pollutants. Novel processes, especially advanced oxidation processes (AOPs), are becoming increasingly extensively studied in BW treatment because of their high efficiency, especially for the removal of micropollutants and pathogens. This review could serve as an instructive guidance for the design and optimization of BW treatment technologies, aiming to help in the fulfilment of sustainable human excreta management.

SARS-CoV-2 Monitoring in Wastewater Reveals Novel Variants and Biomarkers of Infection

Wastewater-based epidemiology (WBE) is a popular tool for the early indication of community spread of infectious diseases. WBE emerged as an effective tool during the COVID-19 pandemic and has provided meaningful information to minimize the spread of infection. Here, we present a combination of analyses using the correlation of viral gene copies with clinical cases, sequencing of wastewater-derived RNA for the viral mutants, and correlative analyses of the viral gene copies with the bacterial biomarkers. Our study provides a unique platform for potentially using the WBE-derived results to predict the spread of COVID-19 and the emergence of new variants of concern. Further, we observed a strong correlation between the presence of SARS-CoV-2 and changes in the microbial community of wastewater, particularly the significant changes in bacterial genera belonging to the families of Lachnospiraceae and Actinomycetaceae. Our study shows that microbial biomarkers could be utilized as prediction tools for future infectious disease surveillance and outbreak responses. Overall, our comprehensive analyses of viral spread, variants, and novel bacterial biomarkers will add significantly to the growing body of literature on WBE and COVID-19.