Evaluation of HA negatively charged membranes in the recovery of human adenoviruses and hepatitis A virus in different water matrices

Quantitative detection of human adenovirus from river water by monolithic adsorption filtration and quantitative PCR

Water contaminated with fecally derived viruses, also known as enteric viruses, represents a particularly high risk for human health. However, they have not been included in water quality regulations yet. The detection of these viruses is often more expensive and time-consuming compared to the analysis of conventional fecal indicator organisms. In addition, most methods are not sensitive enough to detect small viral loads that may already cause serious health issues if present in water. In this study, we established a workflow for the successful and direct enrichment of human adenovirus (HAdV) from artificially contaminated river water based on monolithic adsorption filtration (MAF) and quantitative polymerase reaction (qPCR). With a clear focus on efficiency, we used targeted synthetic DNA fragments as standard for the quantification of HAdV by qPCR, leading to accurate and robust results with a qPCR efficiency of 95 %, a broad working range over 6 orders of magnitude and an LOD of 1 GU/μL. We carried out a cascade of spiking experiments, enhancing the complexity of the spiking matrix with each step to progressively evaluate MAF for the direct concentration of HAdV. We found that negatively charged MAF using monoliths with hydroxyl groups (MAF-OH) showed a better reproducibility and a significantly faster turnaround time than skimmed milk flocculation (SMF) when concentrating HAdV35 from artificially contaminated, acidified mineral water. We then validated positively charged MAF using monoliths with diethyl aminoethyl groups (MAF-DEAE) for the direct concentration of HAdV5 without pre-conditioning of water samples using tap water as spiking matrix with a less defined and controlled water chemistry. Finally, we evaluated MAF-DEAE for the direct concentration of HAdV5 from surface water using river water as representative matrix with an undefined water chemistry. We found, that MAF-DEAE achieved reproducible recoveries of HAdV5, independently of the spiked concentration level or sample volume. Furthermore, we showed, that MAF-DEAE drastically reduced the limit of detection (LOD) of HAdV5 by a factor of 115 from 6.0 ∙ 10³ GU/mL before to 5.2 ∙ 10¹ GU/mL after MAF-DEAE. We identified that recoveries increased for smaller processing volumes with a peak at 0.5 L of 84.0 % and showed that recovery efficiency depends on sample volume and matrix type. The here presented workflow based on MAF-DEAE and qPCR offers an easy-to-implement and highly efficient alternative to existing approaches and allows for a fast detection of HAdV in water.

First confirmed detection of SARS-CoV-2 in untreated wastewater in Australia: A proof of concept for the wastewater surveillance of COVID-19 in the community

Infection with SARS-CoV-2, the etiologic agent of the ongoing COVID-19 pandemic, is accompanied by the shedding of the virus in stool. Therefore, the quantification of SARS-CoV-2 in wastewater affords the ability to monitor the prevalence of infections among the population via wastewater-based epidemiology (WBE). In the current work, SARS-CoV-2 RNA was concentrated from wastewater in a catchment in Australia and viral RNA copies were enumerated using reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) resulting in two positive detections within a six day period from the same wastewater treatment plant (WWTP). The estimated viral RNA copy numbers observed in the wastewater were then used to estimate the number of infected individuals in the catchment via Monte Carlo simulation. Given the uncertainty and variation in the input parameters, the model estimated a median range of 171 to 1,090 infected persons in the catchment, which is in reasonable agreement with clinical observations. This work highlights the viability of WBE for monitoring infectious diseases, such as COVID-19, in communities. The work also draws attention to the need for further methodological and molecular assay validation for enveloped viruses in wastewater.

Low occurrence of Hepatitis A virus in water samples from an urban area of Southern Brazil

Hepatitis A virus (HAV), a member of Picornaviridae family, is the main causative agent of acute viral hepatitis in the world, mainly in developing countries. HAV may be present in contaminated water and food and its presence is often associated to a lesser extent with socioeconomic factors and environmental quality. The main goals in the present study were to standardize a cell culture combined to a polymerase chain reaction protocol for the detection and quantification of viral viability and analyze whether the virus could be found in water samples collected in four urban streams of Sinos River watershed. Virus recovery was assayed from known virus concentrations measured in experimentally contaminated raw and ultrapure water (MilliQ^®). Recovery rates ranged from 270% in raw water to 15,000% in ultrapure water. In a second step, a qPCR coupled to a previous passage in cells, demonstrated more analytical sensitivity when compared to samples assayed without a previous passage in cell cultures. HAV genome was detected in only 1 of 84 samples analyzed, pointing to a very low occurrence of HAV in water samples in the studied region. These findings are remarkable, since no more than 5% of the domestic sewage in this area is treated pointing to a low occurrence of HAV in the population living nearby during the study period.

Enteric viruses' dissemination in a private reserve of natural heritage

This study aimed to assess anthropogenic impact of surrounding population in the Private Reserve of Natural Heritage at Pantanal, the world's largest freshwater wetland ecosystem located in the centre of South America. Viral aetiological agents of acute gastroenteritis as rotavirus A (RVA), noroviruses, human adenoviruses, klassevirus and of hepatitis, as hepatitis A virus, were investigated in different aquatic matrices. Annual collection campaigns were carried out from 2009 to 2012, alternating dry and rainy seasons. Viral particles present in the samples were concentrated by the adsorption-elution method, with negatively charged membranes, and detected by qualitative and quantitative PCR. From a total of 43 samples at least one virus was detected in 65% (28) of them. Viruses were detected in all matrices with concentrations ranging from 2 × 10² to 8·3 × 10⁴ genome copies per litre. A significant higher RVA frequency was observed in the dry season. Our data revealing dissemination of human enteric viruses in water matrices both inside and outside the reserve could be useful to trace faecal contamination in the environment and to minimize the risk of infection by exposure of susceptible individuals.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study is part of a collaborative project designed to investigate the environmental and health conditions of the Private Reserve of Natural Heritage at Pantanal, the largest seasonally flooded wetland in the world. The project aimed to promote health and quality of human and wildlife extending technical-scientific knowledge about pathogens present in the region. By assessing the occurrence of human enteric viruses in different water matrices we demonstrated the anthropogenic impact of surrounding population and pointed out the potential risk of infection by exposure of susceptible individuals.

Recovery rate of multiple enteric viruses artificially seeded in water and concentrated by adsorption-elution with negatively charged membranes: interaction and interference between different virus species

Viral concentration method by adsorption-elution with negative membranes has been widely employed for concentrating viruses from environmental samples. In order to provide an adequate assessment of its recovery efficiency, this study was conducted to assess viral recovery rates for viral species commonly found in water (HAdV-5, EV, RV, BAdV and CAV-2), quantifying viral genomes at the end of the five different steps of the process. Recovery rates were analyzed for several viruses combined in a single water sample and for each virus assayed separately. Ultrapure water samples were artificially contaminated and analyzed by real-time quantitative polymerase chain reaction (qPCR). High recovery rates were found after the final stage when assessed individually (89 to 125%) and combined in the same sample (23 to > 164%). HAdV-5 exhibited >100% recovery when assayed with human viruses and other AdVs, whereas BAdV and CAV-2 were not detected. These data suggest that recovery efficiency could be related to viral structural characteristics, their electric charges and other interactions, so that they are retained with greater or lesser efficiency when coupled. This protocol could be applied to environmental samples, since high recovery rates were observed and infectious viruses were detected at the end of the concentration process.

Comparison of ZetaPlus 60S and nitrocellulose membrane filters for the simultaneous concentration of F-RNA coliphages, porcine teschovirus and porcine adenovirus from river water

Increasing attention is being paid to the impact of agricultural activities on water quality to understand the impact on public health. F-RNA coliphages have been proposed as viral indicators of fecal contamination while porcine teschovirus (PTV) and porcine adenovirus (PAdV) are proposed indicators of fecal contamination of swine origin. Viruses and coliphages are present in water in very low concentrations and must be concentrated to permit their detection. There is little information comparing the effectiveness of the methods for concentrating F-RNA coliphages with concentration methods for other viruses and vice versa. The objective of this study was to compare 5 current published methods for recovering F-RNA coliphages, PTV and PAdV from river water samples concentrated by electronegative nitrocellulose membrane filters (methods A and B) or electropositive Zeta Plus 60S filters (methods C-E). Method A is used routinely for the detection of coliphages (Méndez et al., 2004) and method C (Brassard et al., 2005) is the official method in Health Canada's compendium for the detection of viruses in bottled mineral or spring water. When river water was inoculated with stocks of F-RNA MS2, PAdV, and PTV to final concentrations of 1×10(6) PFU/100 mL, 1×10(5) gc/100 mL and 3×10(5) gc/100 mL, respectively, a significantly higher recovery for each virus was consistently obtained for method A with recoveries of 52% for MS2, 95% for PAdV, and 1.5% for PTV. When method A was compared with method C for the detection of F-coliphages, PAdV and PTV in river water samples, viruses were detected with higher frequencies and at higher mean numbers with method A than with method C. With method A, F-coliphages were detected in 11/12 samples (5-154 PFU/100 mL), PTV in 12/12 samples (397-10,951 gc/100 mL), PAdV in 1/12 samples (15 gc/100 mL), and F-RNA GIII in 1/12 samples (750 gc/100 mL) while F-RNA genotypes I, II, and IV were not detected by qRT-PCR.

Effects of rainfall events on the occurrence and detection efficiency of viruses in river water impacted by combined sewer overflows

Rainfall events can introduce large amount of microbial contaminants including human enteric viruses into surface water by intermittent discharges from combined sewer overflows (CSOs). The present study aimed to investigate the effect of rainfall events on viral loads in surface waters impacted by CSO and the reliability of molecular methods for detection of enteric viruses. The reliability of virus detection in the samples was assessed by using process controls for virus concentration, nucleic acid extraction and reverse transcription (RT)-quantitative PCR (qPCR) steps, which allowed accurate estimation of virus detection efficiencies. Recovery efficiencies of poliovirus in river water samples collected during rainfall events (<10%) were lower than those during dry weather conditions (>10%). The log10-transformed virus concentration efficiency was negatively correlated with suspended solid concentration (r(2)=0.86) that increased significantly during rainfall events. Efficiencies of DNA extraction and qPCR steps determined with adenovirus type 5 and a primer sharing control, respectively, were lower in dry weather. However, no clear relationship was observed between organic water quality parameters and efficiencies of these two steps. Observed concentrations of indigenous enteric adenoviruses, GII-noroviruses, enteroviruses, and Aichi viruses increased during rainfall events even though the virus concentration efficiency was presumed to be lower than in dry weather. The present study highlights the importance of using appropriate process controls to evaluate accurately the concentration of water borne enteric viruses in natural waters impacted by wastewater discharge, stormwater, and CSOs.

Performance of viruses and bacteriophages for fecal source determination in a multi-laboratory, comparative study

An inter-laboratory study of the accuracy of microbial source tracking (MST) methods was conducted using challenge fecal and sewage samples that were spiked into artificial freshwater and provided as unknowns (blind test samples) to the laboratories. The results of the Source Identification Protocol Project (SIPP) are presented in a series of papers that cover 41 MST methods. This contribution details the results of the virus and bacteriophage methods targeting human fecal or sewage contamination. Human viruses used as source identifiers included adenoviruses (HAdV), enteroviruses (EV), norovirus Groups I and II (NoVI and NoVII), and polyomaviruses (HPyVs). Bacteriophages were also employed, including somatic coliphages and F-specific RNA bacteriophages (FRNAPH) as general indicators of fecal contamination. Bacteriophage methods targeting human fecal sources included genotyping of FRNAPH isolates and plaque formation on bacterial hosts Enterococcus faecium MB-55, Bacteroides HB-73 and Bacteroides GB-124. The use of small sample volumes (≤50 ml) resulted in relatively insensitive theoretical limits of detection (10-50 gene copies or plaques × 50 ml(-1)) which, coupled with low virus concentrations in samples, resulted in high false-negative rates, low sensitivity, and low negative predictive values. On the other hand, the specificity of the human virus methods was generally close to 100% and positive predictive values were ∼40-70% with the exception of NoVs, which were not detected. The bacteriophage methods were generally much less specific toward human sewage than virus methods, although FRNAPH II genotyping was relatively successful, with 18% sensitivity and 85% specificity. While the specificity of the human virus methods engenders great confidence in a positive result, better concentration methods and larger sample volumes must be utilized for greater accuracy of negative results, i.e. the prediction that a human contamination source is absent.

Recovery comparison of two virus concentration methods from wastewater using cell culture and real-time PCR

Enteric viruses are shed in the feces and may be present in environmental waters. Their detection in wastewater, even at low concentration, is a major challenge. In this study, recoveries of Echovirus 7 (EV7), virions and RNA in wastewater, using virus concentration methods were determined to evaluate the detection of infectious viruses and the possibility of recovering viral genomes. Two virus concentration methods, PEG precipitation method and two-phase separation method, were applied to recovery experiments of EV7-virions from wastewater, in parallel with recovery experiments of EV7 RNA. The titration of EV7 virions was carried out by cell culture using human rhabdomyosarcoma tumor tissue and the EV7 RNA quantification was performed by real-time PCR. The mean recovery yields of EV7 virions using the PEG precipitation method and the two-phase separation method were 78.5 ± 10.99 and 83.1 ± 0.28 %, respectively. Besides, EV7 RNA recoveries obtained using the PEG precipitation method were four times higher than those using the two-phase separation method. According to our results, the two methods enable to concentrate both infectious viruses and viral genomes. Moreover, considering the protocol time and cost together with the ratio of the EV7 virion recovery to the EV7 RNA recovery, the two-phase separation method (83.1/2.71 %, or 30.6) seems to be more appropriate for selective concentration of viral virions than the PEG precipitation method (78.5/10.33 %, or 7.6).

One-year weekly survey of noroviruses and enteric adenoviruses in the Tone River water in Tokyo metropolitan area, Japan

To investigate the actual fluctuations in the concentrations of noroviruses (NoVs) GI and GII, and enteric adenoviruses (EAdVs) in river water and its relationship with the number of acute infectious gastroenteritis patients, one-year weekly quantitative monitoring of NoVs GI and GII and EAdVs was performed in the Tone River in Japan where the surface water is utilized for the main production of drinking water for the Tokyo Metropolitan Area from October 2009 to September 2010. Noroviruses GI and GII and EAdVs were detected in 28 (54%), 33 (63%), and 23 (44%) of the 52 samples (1 L each), respectively. The concentrations of NoVs GI and GII and EAdVs fluctuated strongly and were more abundant in winter and early spring. The concentration of NoVs GI was transiently greater than 10,000 copies/L. The number of acute infectious gastroenteritis patients in the upper river basin was highly correlated with all the viral concentrations, while general microbial indicator data such as turbidity and heterotrophic plate count were independent of viral concentration as suggested in previous studies. To the best of our knowledge, this is the first study that clearly shows the strong correlation of the number of gastroenteritis with virus contamination in lower river basin.