A comparison of four commercially available RNA extraction kits for wastewater surveillance of SARS-CoV-2 in a college population

The Impact of Viral Concentration Method on Quantification and Long Amplicon Nanopore Sequencing of SARS-CoV-2 and Noroviruses in Wastewater

Wastewater-based surveillance has gained attention in the four years following the start of the COVID-19 pandemic. Accurate pathogen detection, quantification and characterisation rely on the selection of appropriate methodologies. Here, we explore the impact of viral concentration method on RT-qPCR inhibition and quantification of norovirus genogroups I and II (GI and GII), crAssphage, phi6 and SARS-CoV-2. Additionally, their impact on long amplicon sequencing for typing noroviruses and whole-genome sequencing (WGS) SARS-CoV-2 was explored. RT-qPCR inhibition for each viral concentration method was significantly different apart from the two ultrafiltration methods, InnovaPrep® concentrating pipette (IP) and Vivaspin® (VS) centrifugal concentrators. Using an ultrafiltration method reduced inhibition by 62.0% to 96.0% compared to the ammonium sulphate (AS) and polyethylene glycol (PEG) precipitation-based methods. Viral quantification was significantly impacted by concentration method with the highest concentrations (copies/L) observed for VS with 7.2- to 83.2-fold differences from AS depending on the target. Norovirus long amplicon sequencing showed genotype-dependent differences with IP performing best for GI and VS for GII although IP performance gains for GI were relatively small. VS outperformed AS and IP across all metrics during SARS-CoV-2 WGS. Overall, VS performed the best when considering all the areas of investigation.

A Narrative Review of High Throughput Wastewater Sample Processing for Infectious Disease Surveillance: Challenges, Progress, and Future Opportunities

During the recent COVID-19 pandemic, wastewater-based epidemiological (WBE) surveillance played a crucial role in evaluating infection rates, analyzing variants, and identifying hot spots in a community. This expanded the possibilities for using wastewater to monitor the prevalence of infectious diseases. The full potential of WBE remains hindered by several factors, such as a lack of information on the survival of pathogens in sewage, heterogenicity of wastewater matrices, inconsistent sampling practices, lack of standard test methods, and variable sensitivity of analytical techniques. In this study, we review the aforementioned challenges, cost implications, process automation, and prospects of WBE for full-fledged wastewater-based community health screening. A comprehensive literature survey was conducted using relevant keywords, and peer reviewed articles pertinent to our research focus were selected for this review with the aim of serving as a reference for research related to wastewater monitoring for early epidemic detection.

Comparison of Different Reverse Transcriptase-Polymerase Chain Reaction-Based Methods for Wastewater Surveillance of SARS-CoV-2: Exploratory Study

BACKGROUND

Many countries have applied the wastewater surveillance of the COVID-19 pandemic to their national public health monitoring measures. The most used methods for detecting SARS-CoV-2 in wastewater are quantitative reverse transcriptase-polymerase chain reaction (RT-qPCR) and reverse transcriptase-droplet digital polymerase chain reaction (RT-ddPCR). Previous comparison studies have produced conflicting results, thus more research on the subject is required.

OBJECTIVE

This study aims to compare RT-qPCR and RT-ddPCR for detecting SARS-CoV-2 in wastewater. It also aimed to investigate the effect of changes in the analytical pipeline, including the RNA extraction kit, RT-PCR kit, and target gene assay, on the results. Another aim was to find a detection method for low-resource settings.

METHODS

We compared 2 RT-qPCR kits, TaqMan RT-qPCR and QuantiTect RT-qPCR, and RT-ddPCR based on sensitivity, positivity rates, variability, and correlation of SARS-CoV-2 gene copy numbers in wastewater to the incidence of COVID-19. Furthermore, we compared 2 RNA extraction methods, column- and magnetic-bead-based. In addition, we assessed 2 target gene assays for RT-qPCR, N1 and N2, and 2 target gene assays for ddPCR N1 and E. Reverse transcription strand invasion-based amplification (RT-SIBA) was used to detect SARS-CoV-2 from wastewater qualitatively.

RESULTS

Our results indicated that the most sensitive method to detect SARS-CoV-2 in wastewater was RT-ddPCR. It had the highest positivity rate (26/30), and its limit of detection was the lowest (0.06 gene copies/µL). However, we obtained the best correlation between COVID-19 incidence and SARS-CoV-2 gene copy number in wastewater using TaqMan RT-qPCR (correlation coefficient [CC]=0.697, P<.001). We found a significant difference in sensitivity between the TaqMan RT-qPCR kit and the QuantiTect RT-qPCR kit, the first having a significantly lower limit of detection and a higher positivity rate than the latter. Furthermore, the N1 target gene assay was the most sensitive for both RT-qPCR kits, while no significant difference was found between the gene targets using RT-ddPCR. In addition, the use of different RNA extraction kits affected the result when the TaqMan RT-qPCR kit was used. RT-SIBA was able to detect SARS-CoV-2 RNA in wastewater.

CONCLUSIONS

As our study, as well as most of the previous studies, has shown RT-ddPCR to be more sensitive than RT-qPCR, its use in the wastewater surveillance of SARS-CoV-2 should be considered, especially if the amount of SARS-CoV-2 circulating in the population was low. All the analysis steps must be optimized for wastewater surveillance as our study showed that all the analysis steps including the compatibility of the RNA extraction, the RT-PCR kit, and the target gene assay influence the results. In addition, our study showed that RT-SIBA could be used to detect SARS-CoV-2 in wastewater if a qualitative result is sufficient.

Improved SARS-CoV-2 RNA recovery in wastewater matrices using a CTAB-based extraction method

Wastewater-based epidemiology has allowed tracking the magnitude and distribution of SARS-CoV-2 in communities, allowing public health officials to prepare for impending outbreaks. While many factors influence recovery of SARS-CoV-2 from wastewater, proper extraction, concentration, and purification of RNA are key steps to ensure accurate detection of viral particles. The aim of this study was to compare the efficiency of four commonly used RNA extraction methods for detection of the SARS-CoV-2 RNA genome in sewage samples artificially inoculated with the virus, in order to identify a protocol that improves viral recovery. These methods included CTAB-based, TRIzol-based, and guanidinium thiocyanate (GTC)-based extraction procedures coupled with silica spin column-based purification, and an automated extraction/purification protocol using paramagnetic particles. Following RNA extraction, virus recovery rates were compared using RT-qPCR-based detection. The CTAB-based approach yielded the highest recovery rates and was the only method to consistently demonstrate stable virus recovery percentages regardless of the specific physicochemical characteristics of the samples tested. The TRIzol method proved to be the second most effective, yielding significantly higher recovery rates compared to both the GTC-based and the automated extraction methods. These results suggest that the CTAB-based approach could be a useful tool for the recovery of viral RNA from complex wastewater matrices.

Wastewater surveillance beyond COVID-19: a ranking system for communicable disease testing in the tri-county Detroit area, Michigan, USA

Introduction

Throughout the coronavirus disease 2019 (COVID-19) pandemic, wastewater surveillance has been utilized to monitor the disease in the United States through routine national, statewide, and regional monitoring projects. A significant canon of evidence was produced showing that wastewater surveillance is a credible and effective tool for disease monitoring. Hence, the application of wastewater surveillance can extend beyond monitoring SARS-CoV-2 to encompass a diverse range of emerging diseases. This article proposed a ranking system for prioritizing reportable communicable diseases (CDs) in the Tri-County Detroit Area (TCDA), Michigan, for future wastewater surveillance applications at the Great Lakes Water Authority's Water Reclamation Plant (GLWA's WRP).

Methods

The comprehensive CD wastewater surveillance ranking system (CDWSRank) was developed based on 6 binary and 6 quantitative parameters. The final ranking scores of CDs were computed by summing the multiplication products of weighting factors for each parameter, and then were sorted based on decreasing priority. Disease incidence data from 2014 to 2021 were collected for the TCDA. Disease incidence trends in the TCDA were endowed with higher weights, prioritizing the TCDA over the state of Michigan.

Results

Disparities in incidences of CDs were identified between the TCDA and state of Michigan, indicating epidemiological differences. Among 96 ranked CDs, some top ranked CDs did not present relatively high incidences but were prioritized, suggesting that such CDs require significant attention by wastewater surveillance practitioners, despite their relatively low incidences in the geographic area of interest. Appropriate wastewater sample concentration methods are summarized for the application of wastewater surveillance as per viral, bacterial, parasitic, and fungal pathogens.

Discussion

The CDWSRank system is one of the first of its kind to provide an empirical approach to prioritize CDs for wastewater surveillance, specifically in geographies served by centralized wastewater collection in the area of interest. The CDWSRank system provides a methodological tool and critical information that can help public health officials and policymakers allocate resources. It can be used to prioritize disease surveillance efforts and ensure that public health interventions are targeted at the most potentially urgent threats. The CDWSRank system can be easily adopted to geographical locations beyond the TCDA.

Comparison of the methods for isolation and detection of SARS-CoV-2 RNA in municipal wastewater

Introduction

Coronavirus SARS-CoV-2 is a causative agent responsible for the current global pandemic situation known as COVID-19. Clinical manifestations of COVID-19 include a wide range of symptoms from mild (i.e., cough, fever, dyspnea) to severe pneumonia-like respiratory symptoms. SARS-CoV-2 has been demonstrated to be detectable in the stool of COVID-19 patients. Waste-based epidemiology (WBE) has been shown as a promising approach for early detection and monitoring of SARS-CoV-2 in the local population performed via collection, isolation, and detection of viral pathogens from environmental sources.

Methods

In order to select the optimal protocol for monitoring the COVID-19 epidemiological situation in region Turiec, Slovakia, we (1) compared methods for SARS-CoV-2 separation and isolation, including virus precipitation by polyethylene glycol (PEG), virus purification via ultrafiltration (Vivaspin®) and subsequent isolation by NucleoSpin RNA Virus kit (Macherey-Nagel), and direct isolation from wastewater (Zymo Environ Water RNA Kit); (2) evaluated the impact of water freezing on SARS- CoV-2 separation, isolation, and detection; (3) evaluated the role of wastewater filtration on virus stability; and (4) determined appropriate methods including reverse transcription-droplet digital PCR (RT-ddPCR) and real-time quantitative polymerase chain reaction (RT-qPCR) (targeting the same genes, i.e., RdRp and gene E) for quantitative detection of SARS-CoV-2 in wastewater samples.

Results

(1) Usage of Zymo Environ Water RNA Kit provided superior quality of isolated RNA in comparison with both ultracentrifugation and PEG precipitation. (2) Freezing of wastewater samples significantly reduces the RNA yield. (3) Filtering is counterproductive when Zymo Environ Water RNA Kit is used. (4) According to the specificity and sensitivity, the RT-ddPCR outperforms RT-qPCR.

Discussion

The results of our study suggest that WBE is a valuable early warning alert and represents a non-invasive approach to monitor viral pathogens, thus protects public health on a regional and national level. In addition, we have shown that the sensitivity of testing the samples with a nearer detection limit can be improved by selecting the appropriate combination of enrichment, isolation, and detection methods.

COVID-19 and Water Variables: Review and Scientometric Analysis

COVID-19 has changed the world since 2020, and the field of water specifically, boosting scientific productivity (in terms of published articles). This paper focuses on the influence of COVID-19 on scientific productivity with respect to four water variables: (i) wastewater, (ii) renewable water resources, (iii) freshwater withdrawal, and (iv) access to improved and safe drinking water. The field's literature was firstly reviewed, and then the maps were built, emphasizing the strong connections between COVID-19 and water-related variables. A total of 94 countries with publications that assess COVID-19 vs. water were considered and evaluated for how they clustered. The final step of the research shows that, on average, scientific productivity on the water topic was mostly conducted in countries with lower COVID-19 infection rates but higher development levels as represented by gross domestic product (GDP) per capita and the human development index (HDI). According to the statistical analysis, the water-related variables are highly significant, with positive coefficients. This validates that countries with higher water-related values conducted more research on the relationship with COVID-19. Wastewater and freshwater withdrawal had the highest impact on the scientific productivity with respect to COVID-19. Access to safe drinking water becomes insignificant in the presence of the development parameters.

Adenine imprinted beads as a novel selective extracellular DNA extraction method reveals underestimated prevalence of extracellular antibiotic resistance genes in various environments

Despite severe threats of extracellular antibiotic resistance genes (eARGs) towards public health in various environments, advanced studies have been hindered mainly by ineffective extracellular DNA (exDNA) extraction methods, which is challenged by trace levels of exDNA and inference from abundant coexisting compounds. This study developed a highly selective exDNA extraction method based on molecular imprinting technology (MIT) by using adenine as the template for the first time. Results suggested that adenine imprinted beads were rough spheres at an average size of 0.39 ± 0.07 μm. They effectively adsorbed DNA in the absence of chaotropic agents, with superior capacity (796.2 mg/g), rate (0.0066/s) and regarding DNA of variable lengths, even the ultra-short DNA (<100 bp). They were also highly selective towards DNA, circumventing the interference of competitive compounds' interference. These properties contribute to efficient exDNA extraction (71 %-119 %) from various environmental samples. Specifically, adenine imprinted beads enabled significantly higher extraction rates of eARGs from river, air and vegetable samples (69 %-95 %) compared to that by commercial DNA extraction products (16 %-62 %). The adenine imprinted beads-based method reveals underestimated eARG levels in the environment and the corresponding risks, and thus will thus be a powerful tool for advanced exDNA research.

Evaluation of viral concentration and extraction methods for SARS-CoV-2 recovery from wastewater using droplet digital and quantitative RT-PCR

The ongoing pandemic caused by the emergence of SARS-CoV-2 has resulted in millions of deaths worldwide despite the various measures announced by the authorities. Wastewater-based epidemiology has the ability to provide a day-to-day estimation of the number of infected people in a fast and cost-effective manner. However, owing to the complex nature of wastewater, wastewater monitoring for viral genome copies is affected by the extensive viral fragmentation that takes place all the way to the sewage and the analytical lab. The aim of this study was to evaluate different methodologies for the concentration and extraction of viruses in wastewaters and to select and improve an option that maximizes the recovery of SARS-CoV-2. We compare 5 different concentration methods and 4 commercially available kits for the RNA extraction. To evaluate the performance and the recovery of these, SARS-CoV-2 isolated from patients was used as a spike control. Additionally, the presence of SARS-CoV-2 in all wastewater samples was determined using reverse transcription quantitative PCR (RT-qPCR) and reverse transcription droplet digital PCR (RT-ddPCR), targeting three genetic markers (N1, N2 and N3). Using spiked samples, recoveries were estimated 2.1-37.6% using different extraction kits and 0.1-2.1% using different concentration kits. It was found that a direct capture-based method, evaluated against a variety of concentration methods, is the best in terms of recovery, time and cost. Interestingly, we noticed a good agreement between the results provided by RT-qPCR and RT-ddPCR in terms of recovery. This evaluation can serve as a guide for laboratories establishing a protocol to perform wastewater monitoring of SARS-CoV-2. Overall, data presented here reinforces the validity of WBE for SARS-CoV-2 surveillance, uncovers potential caveats in the selection of concentration and extraction protocols and points towards optimal solutions to maximize its potential.

Diagnostic Approaches For COVID-19: Lessons Learned and the Path Forward

Coronavirus disease 2019 (COVID-19) is a transmitted respiratory disease caused by the infection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although humankind has experienced several outbreaks of infectious diseases, the COVID-19 pandemic has the highest rate of infection and has had high levels of social and economic repercussions. The current COVID-19 pandemic has highlighted the limitations of existing virological tests, which have failed to be adopted at a rate to properly slow the rapid spread of SARS-CoV-2. Pandemic preparedness has developed as a focus of many governments around the world in the event of a future outbreak. Despite the largely widespread availability of vaccines, the importance of testing has not diminished to monitor the evolution of the virus and the resulting stages of the pandemic. Therefore, developing diagnostic technology that serves as a line of defense has become imperative. In particular, that test should satisfy three criteria to be widely adopted: simplicity, economic feasibility, and accessibility. At the heart of it all, it must enable early diagnosis in the course of infection to reduce spread. However, diagnostic manufacturers need guidance on the optimal characteristics of a virological test to ensure pandemic preparedness and to aid in the effective treatment of viral infections. Nanomaterials are a decisive element in developing COVID-19 diagnostic kits as well as a key contributor to enhance the performance of existing tests. Our objective is to develop a profile of the criteria that should be available in a platform as the target product. In this work, virus detection tests were evaluated from the perspective of the COVID-19 pandemic, and then we generalized the requirements to develop a target product profile for a platform for virus detection.

Useful molecular tools for facing next pandemic events: Effective sample preparation and improved RT-PCR for highly sensitive detection of SARS-CoV-2 in wastewater environment

Viral pandemics can be inevitable in the next future. Considering SARS-CoV-2 pandemics as an example, there seems to be a need to develop a surveillance system able to monitor the presence of potential pathogenic agents. The sewage and wastewater environments demonstrated to be suitable targets for such kind of analysis. In addition, it is important to have reliable molecular diagnostic tools and also to develop a robust detection strategy. In this study, an effective sample preparation procedure was selected from four options and combined with a newly developed improved RT-PCR. First, a model viral system was constructed, containing a fragment of the SARS-CoV-2 gene encoding for the Spike protein. The encapsidated S RNA mimic (ESRM) was based on the plum pox virus (PPV) genome with the inserted targeted gene fragment. ESRM was used for seeding wastewater samples in order to evaluate the viral recovery of four different viral RNA concentration/extraction methods. The efficiency of individual approaches was assessed by the use of a quantitative reverse transcription PCR (qRT-PCR) and by a one-step single-tube nested quantitative reverse transcription PCR (OSN-qRT-PCR). For the detection of viruses in wastewater samples with low viral loads, OSN-qRT-PCR assay produced the most satisfactory results and the highest sensitivity.

Evaluation of multiple analytical methods for SARS-CoV-2 surveillance in wastewater samples

In this study, 14 virus concentration protocols based on centrifugation, filtration, polyethylene glycol (PEG) precipitation and ultrafiltration were tested for their efficacy for the quantification of SARS-CoV-2 in wastewater samples. These protocols were paired with four RNA extraction procedures resulting in a combination of 50 unique approaches. Bovine respiratory syncytial virus (BRSV) was used as a process control and seeded in each wastewater sample subjected to all 50 protocols. The recovery of BRSV obtained through the application of 50 unique approaches ranged from <0.03 to 64.7% (±1.6%). Combination of centrifugation as the solid removal step, ultrafiltration (Amicon-UF-15; 100 kDa cut-off; protocol 9) as the primary virus concentration method, and Zymo Quick-RNA extraction kit provided the highest BRSV recovery (64.7 ± 1.6%). To determine the impact of prolonged storage of large wastewater sample volume (900 mL) at -20 °C on enveloped virus decay, the BRSV seeded wastewaters samples were stored at -20 °C up to 110 days and analyzed using the most efficient concentration (protocol 9) and extraction (Zymo Quick-RNA kit) methods. BRSV RNA followed a first-order decay rate (k = 0.04/h with r2 = 0.99) in wastewater. Finally, 21 wastewater influent samples from five wastewater treatment plants (WWTPs) in southern Maryland, USA were analyzed between May to August 2020 to determine SARS-CoV-2 RNA concentrations. SARS-CoV-2 RNA was quantifiable in 17/21 (81%) of the influent wastewater samples with concentration ranging from 1.10 (±0.10) × 104 to 2.38 (±0.16) × 106 gene copies/L. Among the RT-qPCR assays tested, US CDC N1 assay was the most sensitive followed by US CDC N2, E_Sarbeco, and RdRp assays. Data presented in this study may enhance our understanding on the effective concentration and extraction of SARS-CoV-2 from wastewater.