Concentration and purification of beef extract mock eluates from water samples for the detection of enteroviruses, hepatitis A virus, and Norwalk virus by reverse transcription-PCR

An ELIME assay for hepatitis A virus detection

An Enzyme Linked ImmunoMagnetic Electrochemical assay (ELIME) was developed for the detection of the hepatitis A virus (HAV). This system is based on the use of new polydopamine-modified magnetic nanobeads as solid support for the immunochemical chain, and an array of 8 screen-printed electrodes as a sensing platform. Enzymatic-by-product is quickly measured by differential pulse voltammetry. For this purpose, all analytical parameters were optimized; in particular, different blocking reagents were evaluated in order to minimize the nonspecific interaction of bioreagents. Using the ELIME assays, a quantitative determination of HAV can be achieved with a detection limit of 1·10^-11 IU mL^-1 and a working range between 10^-10 - 5 × 10^-7 IU mL^-1. The cross-reactivity of the commercial monoclonal antibodies against HAV used in ELIME assays was tested for Coxsackie B4, resulting very low. The sensitivity was also investigated and compared with spectrophotometric sandwich ELISA. The average relative standard deviation (RSD) of the ELIME method was less than 5% for the assays performed on the same day, and 7% for the measurements made on different days. The proposed system was applied to the cell culture of HAV, which title was quantified by Real-Time Quantitative Reverse Transcription PCR (RT¬qPCR). To compare the results, a correlation between the units used in ELIME (IU mL^-1) and those used in RT¬qPCR (genome mL^-1) was established using a HAV-positive sample, resulting in 1 IU mL^-1-10^-4 gen mL^-1 (R² = 0.978). The ELIME tool exhibits good stability and high biological selectivity for HAV antigen detection and was successfully applied for the determination of HAV in tap water.

Transcriptomic determinants of the response of ST-111 Pseudomonas aeruginosa AG1 to ciprofloxacin identified by a top-down systems biology approach

Pseudomonas aeruginosa is an opportunistic pathogen that thrives in diverse environments and causes a variety of human infections. Pseudomonas aeruginosa AG1 (PaeAG1) is a high-risk sequence type 111 (ST-111) strain isolated from a Costa Rican hospital in 2010. PaeAG1 has both blaVIM-2 and blaIMP-18 genes encoding for metallo-β-lactamases, and it is resistant to β-lactams (including carbapenems), aminoglycosides, and fluoroquinolones. Ciprofloxacin (CIP) is an antibiotic commonly used to treat P. aeruginosa infections, and it is known to produce DNA damage, triggering a complex molecular response. In order to evaluate the effects of a sub-inhibitory CIP concentration on PaeAG1, growth curves using increasing CIP concentrations were compared. We then measured gene expression using RNA-Seq at three time points (0, 2.5 and 5 h) after CIP exposure to identify the transcriptomic determinants of the response (i.e. hub genes, gene clusters and enriched pathways). Changes in expression were determined using differential expression analysis and network analysis using a top–down systems biology approach. A hybrid model using database-based and co-expression analysis approaches was implemented to predict gene–gene interactions. We observed a reduction of the growth curve rate as the sub-inhibitory CIP concentrations were increased. In the transcriptomic analysis, we detected that over time CIP treatment resulted in the differential expression of 518 genes, showing a complex impact at the molecular level. The transcriptomic determinants were 14 hub genes, multiple gene clusters at different levels (associated to hub genes or as co-expression modules) and 15 enriched pathways. Down-regulation of genes implicated in several metabolism pathways, virulence elements and ribosomal activity was observed. In contrast, amino acid catabolism, RpoS factor, proteases, and phenazines genes were up-regulated. Remarkably, > 80 resident-phage genes were up-regulated after CIP treatment, which was validated at phenomic level using a phage plaque assay. Thus, reduction of the growth curve rate and increasing phage induction was evidenced as the CIP concentrations were increased. In summary, transcriptomic and network analyses, as well as the growth curves and phage plaque assays provide evidence that PaeAG1 presents a complex, concentration-dependent response to sub-inhibitory CIP exposure, showing pleiotropic effects at the systems level. Manipulation of these determinants, such as phage genes, could be used to gain more insights about the regulation of responses in PaeAG1 as well as the identification of possible therapeutic targets. To our knowledge, this is the first report of the transcriptomic analysis of CIP response in a ST-111 high-risk P. aeruginosa strain, in particular using a top-down systems biology approach.

Impact of beef extract used for sample concentration on the detection of Escherichia coli DNA in water samples via qPCR

There is increasing interest in methodologies for the simultaneous concentration and detection of multiple targets in individual samples. The aim of this study was to investigate the potential presence of E. coli DNA in beef extract powder used as part of a procedure to concentrate water samples for the simultaneous detection of bacteria, viruses and protozoa. DNA from E. coli was detected in five out of six beef extract lots tested, demonstrating the limitations of its inclusion when being used in assays that will be used for the detection of E. coli in water samples. Further work is required to clarify if this phenomenon also occurs for other microorganisms of interest in water.

Evaluation of Secondary Concentration Methods for Poliovirus Detection in Wastewater

Effective surveillance of human enteric viruses is critical to estimate disease prevalence within a community and can be a vital supplement to clinical surveillance. This study sought to evaluate simple, effective, and inexpensive secondary concentration methods for use with ViroCap™ filter eluate for environmental surveillance of poliovirus. Wastewater was primary concentrated using cartridge ViroCap filters, seeded with poliovirus type 1 (PV1), and then concentrated using five secondary concentration methods (beef extract-Celite, ViroCap flat disc filter, InnovaPrep® Concentrating Pipette, polyethylene glycol [PEG]/sodium chloride [NaCl] precipitation, and skimmed-milk flocculation). PV1 was enumerated in secondary concentrates by plaque assay on BGMK cells. Of the five tested methods, PEG/NaCl precipitation and skimmed-milk flocculation resulted in the highest PV1 recoveries. Optimization of the skimmed-milk flocculation method resulted in a greater PV1 recovery (106 ± 24.8%) when compared to PEG/NaCl precipitation (59.5 ± 19.4%) (p = 0.004, t-test). The high PV1 recovery, short processing time, low reagent cost, no required refrigeration, and requirement for only standard laboratory equipment suggest that the skimmed-milk flocculation method would be a good candidate to be field-validated for secondary concentration of environmental ViroCap filter samples containing poliovirus.

Evaluation of Secondary Concentration Methods for Poliovirus Detection in Wastewater

Effective surveillance of human enteric viruses is critical to estimate disease prevalence within a community and can be a vital supplement to clinical surveillance. This study sought to evaluate simple, effective, and inexpensive secondary concentration methods for use with ViroCap™ filter eluate for environmental surveillance of poliovirus. Wastewater was primary concentrated using cartridge ViroCap filters, seeded with poliovirus type 1 (PV1), and then concentrated using five secondary concentration methods (beef extract-Celite, ViroCap flat disc filter, InnovaPrep® Concentrating Pipette, polyethylene glycol [PEG]/sodium chloride [NaCl] precipitation, and skimmed-milk flocculation). PV1 was enumerated in secondary concentrates by plaque assay on BGMK cells. Of the five tested methods, PEG/NaCl precipitation and skimmed-milk flocculation resulted in the highest PV1 recoveries. Optimization of the skimmed-milk flocculation method resulted in a greater PV1 recovery (106 ± 24.8%) when compared to PEG/NaCl precipitation (59.5 ± 19.4%) (p = 0.004, t-test). The high PV1 recovery, short processing time, low reagent cost, no required refrigeration, and requirement for only standard laboratory equipment suggest that the skimmed-milk flocculation method would be a good candidate to be field-validated for secondary concentration of environmental ViroCap filter samples containing poliovirus.

Improved Detection of Norovirus and Hepatitis A Virus in Surface Water by Applying Pre-PCR Processing

Quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) detection of waterborne RNA viruses generally requires concentration of large water volumes due to low virus levels. A common approach is to use dead-end ultrafiltration followed by precipitation with polyethylene glycol. However, this procedure often leads to the co-concentration of PCR inhibitors that impairs the limit of detection and causes false-negative results. Here, we applied the concept of pre-PCR processing to optimize RT-qPCR detection of norovirus genogroup I (GI), genogroup II (GII), and hepatitis A virus (HAV) in challenging water matrices. The RT-qPCR assay was improved by screening for an inhibitor-tolerant master mix and modifying the primers with twisted intercalating nucleic acid molecules. Additionally, a modified protocol based on chaotropic lysis buffer and magnetic silica bead nucleic acid extraction was developed for complex water matrices. A validation of the modified extraction protocol on surface and drinking waters was performed. At least a 26-fold improvement was seen in the most complex surface water studied. The modified protocol resulted in average recoveries of 33, 13, 8, and 4% for mengovirus, norovirus GI, GII, and HAV, respectively. The modified protocol also improved the limit of detection for norovirus GI and HAV. RT-qPCR inhibition with C _q shifts of 1.6, 2.8, and 3.5 for norovirus GI, GII, and HAV, respectively, obtained for the standard nucleic acid extraction were completely eliminated by the modified protocol. The standard nucleic acid extraction method worked well on drinking water with no RT-qPCR inhibition observed and average recoveries of 80, 124, 89, and 32% for mengovirus, norovirus GI, GII, and HAV, respectively.

In Situ Capture RT-qPCR: A New Simple and Sensitive Method to Detect Human Norovirus in Oysters

Human noroviruses (HuNoVs) are the major cause worldwide for non-bacterial acute gastroenteritis. In this study, we applied a novel viral receptor mediated in situ capture RT-qPCR (ISC-RT-qPCR) to detect HuNoVs in oysters and compared with the traditional RT-qPCR method. Ten HuNoVs RT-PCR positive and 5 negative clinical samples from gastroenteritis patients were used to compare specificity and sensitivity of ISC-RT-qPCR against that of the RT-qPCR assay. ISC-RT-qPCR had at a one-log and a two-log increase in sensitivity over that of the RT-qPCR assay for genotype I (GI) and GII, respectively. Distributions of HuNoVs in oyster tissues were investigated in artificially inoculated oysters. GI HuNoVs could be detected in all tissues in inoculated oysters by both ISC-RT-qPCR and RT-qPCR. GII HuNoVs could only be detected in gills and digestive glands by both methods. The number of viral genomic copies (vgc) measured by ISC-RT-qPCR was comparable with RT-qPCR in the detection of GI and GII HuNoVs in inoculated oysters. Thirty-six oyster samples from local market were assayed for HuNoVs by both assays. More HuNoVs could be detected by ISC-RT-qPCR in retail oysters. The detection rates of GI HuNoVs in gills, digestive glands, and residual tissues were 33.3, 25.0, and 19.4% by ISC-RT-qPCR; and 5.6, 11.1, and 11.1% by RT-qPCR, respectively. The detection rates of GII HuNoVs in gills were 2.8% by ISC-RT-qPCR; no GII HuNoV was detected in these oysters by RT-qPCR. Overall, all results demonstrated that ISC-RT-qPCR is a promising method for detecting HuNoVs in oyster samples.

Comparison of concentration methods for detection of hepatitis A virus in water samples

Hepatitis A virus is a pathogen associated with water pollution. Contaminated drinking water can cause hepatitis A outbreaks, lead to economic losses, and even threaten human lives. It is difficult to detect low levels of hepatitis A virus in water, so the virus must be concentrated in order to quantify it accurately. Here, we present a simple, rapid, efficient technique for the concentration and detection of hepatitis A virus in water. Our data showed that adding phosphate-buffered saline to the water, pre-filtering the water, and adding Trizol reagent directly to the filtration membrane can significantly improve concentration efficiency. Of three types of filtration membranes studied (mixed cellulose ester membrane, polyvinylidene fluoride membrane, and nylon membrane), the concentration efficiency using mixed cellulose ester membrane with a 0.1-μm pore size was the highest, reaching 92.62 ± 5.17%. This method was used to concentrate hepatitis A virus in water samples from Donghu Lake. Using SYBR Green real-time reverse transcription polymerase chain reaction analysis, the detection sensitivity of this method reached 10(1) copies/μL and its concentration efficiency reached 79.45 ± 9.88%.

Evidence of the circulation of hepatitis A virus, subgenotype IA, in environmental samples from Antioquia, Colombia

INTRODUCTION

Hepatitis A virus (HAV) is an important pathogen, typically transmitted via the faecal-oral route. The epidemiology of the infection is directly related to drinking water access and adequate disposal of sewage water. 

OBJECTIVE

To determine the presence and identify the genotype of HAV in environmental samples from eight municipalities and two villages in Antioquia, northwestern Colombia. 

MATERIALS AND METHODS

Three serial samplings were done between December, 2012, and April, 2014. Water samples were obtained from drinking water plants prior to treatment, as well as from the main reserve of wastewater in each municipality included in the study. Viral concentrations for the two types of sample sources were determined by filtration/tangential ultrafiltration and polyethyleneglycol plus flocculation with skimmed milk, respectively. Total ARN was subsequently obtained from each sample and the VP3-VP1 region amplified for detection of the viral genome. The genotype was determined by amplification of the VP1-2B region. 

RESULTS

The HAV genome was detected in samples from drinking water plants at Puerto Berrío, Frontino and Nutibara, and in wastewater samples from the municipalities of Arboletes, Zaragoza and Venecia. HAV subgenotype IA was identified using phylogenetic analysis. 

CONCLUSION

In this study, HAV was identified in 6.6% of the samples from drinking water plants and 13.3% of wastewater samples. This is the first report of HAV subgenotype IA circulating in environmental samples from Antioquia.

Viruses in Water Environment

Development of PCR method had a great impact on studies on viruses in water environment, and now it makes possible to determine various kind of viruses from river, marine water and water/wastewater treatment systems, though there are still needs to improve accuracy of quantification. Now we know that river water may contain 1000copy/L of norovirus. The infectious risk management for recreational water has been left and not updated, hence we need develop better management system based on scientific knowledge.

Comparison of Two Concentration Methods for the Molecular Detection of Enteroviruses in Raw and Treated Sewage

Human enteric viruses are a major causative agent of emerging waterborne diseases and constitute a serious public health concern. Environmental contamination occurs through discharge of waste materials from infected persons. Methods for viral detection should be developed to detect low infective dose of enteric viruses in environment. In this study, we aimed at comparing two concentration methods for the detection of naturally occurring enteroviruses in raw and treated sewage. In the first method, polyethylene glycol is used to concentrate viral particles from the collected samples. The second method is based on ultracentrifugation of viral particles at high speed (110,000×g). Genomes of enteroviruses were quantified by the quantitative real-time PCR method in raw and treated sewage samples. PEG-based method yielded higher genomic copies of enteric viruses (with an average of 5.9 log10 genomic copies/100 mL) when applied to raw sewage samples. While the ultracentrifugation assay in the second method decreases genomic copies number (with an average of 5.4 log10 genomic copies/100 mL). The recovery differences between the two methods were not significant when applied to clean samples (treated sewage). This could be explained by the presence of inhibitors, which interfere with qRT-PCR, in less quantity comparatively to raw sewage. PEG-based method would be more accurate for samples with high-organic matter load. This report emphasizes the importance of matrices nature on the recovery of enteroviruses from sewage samples. This should be taken into consideration for establishing standardized virological assays to ensure the virological quality control of discharged water in environment.

Pathogen Decay during Managed Aquifer Recharge at Four Sites with Different Geochemical Characteristics and Recharge Water Sources

Recycling of stormwater water and treated effluent via managed aquifer recharge (MAR) has often been hampered because of perceptions of low microbiological quality of recovered water and associated health risks. The goal of this study was to assess the removal of selected pathogens in four large-scale MAR schemes and to determine the influence of aquifer characteristics, geochemistry, and type of recharge water on the pathogen survival times. Bacterial pathogens tested in this study had the shortest one log removal time (, <3 d), followed by oocysts (, <120 d), with enteric viruses having the biggest variability in removal times (, 18 to >200 d). Human adenovirus and rotavirus were relatively persistent under anaerobic conditions (, >200 d). Human adenovirus survived longer than all the other enteric virus tested in the study and hence could be used as a conservative indicator for virus removal in groundwater during MAR. The results suggest that site-specific subsurface conditions such as groundwater chemistry can have considerable influence on the decay rates of enteric pathogens and that viruses are likely to be the critical pathogens from a public health perspective.

Concentration of enteric viruses in large volumes of water using a cartridge-type mixed cellulose ester membrane

A viral adsorption-elution method using a flat/disk-type electronegative membrane (diameter of 47-90 mm) has been widely utilized to concentrate viruses in relatively small volumes of water (up to 10 L) due to limited filtration area. In the present study, we aimed to develop a virus concentration method that is based on the same principle and yet allows concentration of large volumes of water using a cartridge-type electronegative membrane. We modified two electronegative membrane-based methods for this purpose (i.e., Mg(2+) method and Al(3+) method) and determined recovery efficiencies of poliovirus and murine norovirus inoculated in water samples. The virus recovery efficiency of the Al(3+) method substantially decreased as the volume of water sample increased. In contrast, Mg(2+) method showed stable virus recovery efficiencies (10-54 %) even when 40 to 1,000 L of river and tap water samples were processed. The volume of the concentrate (400 mL) can be further reduced to 1.5 mL by a Centricon plus-70 centrifugal ultrafiltration device with overall recovery efficiencies of 8.8-16 %. Our results demonstrated that the newly developed virus concentration method enables detection of as low as 10(1) copies/L of viruses in water samples.

Methods for Preparation of MS2 Phage-Like Particles and Their Utilization as Process Control Viruses in RT-PCR and qRT-PCR Detection of RNA Viruses From Food Matrices and Clinical Specimens

RNA viruses are pathogenic agents of many serious infectious diseases affecting humans and animals. The detection of pathogenic RNA viruses is based on modern molecular methods, of which the most widely used methods are the reverse transcription polymerase chain reaction (RT-PCR) and the real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR). All steps of RT-PCR and qRT-PCR should be strictly controlled to ensure the validity of obtained results. False-negative results may be caused not only by inhibition of RT or/and PCR steps but also by failure of the nucleic acid extraction step, particularly in the case of viral RNA extraction. The control of nucleic acid extraction generally involves the utilization of a non-pathogenic virus (process control virus) of similar structural properties to those of the target virus. Although in clinical samples the use of such process control virus is only recommended, in other kinds of settings such as food matrices its use is necessary. Currently, several different process control viruses are used for these purposes. Process control viruses can also be constructed artificially using technology for production of MS2 phage-like particles, which have many advantages in comparison with other used controls and are especially suited for controlling the detection and quantification of certain types of RNA viruses. The technology for production of MS2 phage-like particles is theoretically well established, uses the knowledge gained from the study of the familiar bacteriophage MS2 and utilizes many different approaches for the construction of the various process control viruses. Nevertheless, the practical use of MS2 phage-like particles in routine diagnostics is relatively uncommon. The current situation with regard to the use of MS2 phage-like particles as process control viruses in detection of RNA viruses and different methods of their construction, purification and use are summarized and discussed in this review.

A small volume procedure for viral concentration from water

Small-scale concentration of viruses (sample volumes 1-10 L, here simulated with spiked 100 ml water samples) is an efficient, cost-effective way to identify optimal parameters for virus concentration. Viruses can be concentrated from water using filtration (electropositive, electronegative, glass wool or size exclusion), followed by secondary concentration with beef extract to release viruses from filter surfaces, and finally tertiary concentration resulting in a 5-30 ml volume virus concentrate. In order to identify optimal concentration procedures, two different electropositive filters were evaluated (a glass/cellulose filter [1MDS] and a nano-alumina/glass filter [NanoCeram]), as well as different secondary concentration techniques; the celite technique where three different celite particle sizes were evaluated (fine, medium and large) followed by comparing this technique with that of the established organic flocculation method. Various elution additives were also evaluated for their ability to enhance the release of adenovirus (AdV) particles from filter surfaces. Fine particle celite recovered similar levels of AdV40 and 41 to that of the established organic flocculation method when viral spikes were added during secondary concentration. The glass/cellulose filter recovered higher levels of both, AdV40 and 41, compared to that of a nano-alumina/glass fiber filter. Although not statistically significant, the addition of 0.1% sodium polyphosphate amended beef extract eluant recovered 10% more AdV particles compared to unamended beef extract.

Development of a novel filter cartridge system with electropositive granule media to concentrate viruses from large volumes of natural surface water

Exposure to various infectious viruses in environmental drinking water can constitute a public health risk. However, it is difficult to detect viruses in water due to their low concentration. In this study, we have developed a novel filter cartridge system containing electropositive granule media (EGM). Viruses present in large volumes of environmental samples were adsorbed onto the EGM, and then recovered by elution and poly(ethylene glycol) (PEG) concentration. To evaluate the system's efficiency in viral recovery, poliovirus (PV-1), a surrogate for enteric viruses, was used to artificially contaminate river water samples which were then assayed by quantitative real-time PCR. To optimize the concentration procedure, the eluent type, water flow rate and properties (e.g., pH, bacterial, and viral loads), were evaluated. The highest virus recovery was obtained by pumping river water at a flow rate of 300 mL/min and then pushing 3 L of an eluent containing 3× broth [1.5% (w/v) NaCl, 3% (w/v) tryptone, 1.5% (w/v) beef powder] with 0.05 mol/L glycine through the filter. Using this procedure, the recovery efficiencies of PV-1 from 10 to 100 L of spiked river water were up to 99%. In addition, this method is virus load and pH dependent. Virus recovery was maximal at a load of between 10(3.5) and 10(5.5) TCID50 and a pH ranging from 5 to 7. The bacterial load in the water has no effect on virus recovery. Different types of viruses and surface water were tested to validate the system's applicability. Results revealed that the EGM filter cartridge was able to concentrate PV-1, human adenoviruses (HAdVs) and noroviruses (HuNoVs) with high efficiency from river, lake, and reservoir water. Furthermore, it showed more efficient recovery than glass wool and 1MDS filters. These data suggest that this system provides rapid and efficient virus recovery from a large volume of natural surface water and, as such, could be a useful tool in revealing the presence of viruses in surface water.

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.

A unified method to process biosolids samples for the recovery of bacterial, viral, and helminths pathogens

For land application, biosolids are classified as Class A or Class B based on the levels of bacterial, viral, and helminths pathogens in residual biosolids. The current EPA methods for the detection of these groups of pathogens in biosolids include discrete steps. Therefore, a separate sample is processed independently to quantify the number of each group of the pathogens in biosolids. The aim of the study was to develop a unified method for simultaneous processing of a single biosolids sample to recover bacterial, viral, and helminths pathogens. At the first stage for developing a simultaneous method, nine eluents were compared for their efficiency to recover viruses from a 100 gm spiked biosolids sample. In the second stage, the three top performing eluents were thoroughly evaluated for the recovery of bacteria, viruses, and helminthes. For all three groups of pathogens, the glycine-based eluent provided higher recovery than the beef extract-based eluent. Additional experiments were performed to optimize performance of glycine-based eluent under various procedural factors such as, solids to eluent ratio, stir time, and centrifugation conditions. Last, the new method was directly compared with the EPA methods for the recovery of the three groups of pathogens spiked in duplicate samples of biosolids collected from different sources. For viruses, the new method yielded up to 10% higher recoveries than the EPA method. For bacteria and helminths, recoveries were 74% and 83% by the new method compared to 34% and 68% by the EPA method, respectively. The unified sample processing method significantly reduces the time required for processing biosolids samples for different groups of pathogens; it is less impacted by the intrinsic variability of samples, while providing higher yields (P = 0.05) and greater consistency than the current EPA methods.

Waterborne human pathogenic viruses of public health concern

In recent years, the impending impact of waterborne pathogens on human health has become a growing concern. Drinking water and recreational exposure to polluted water have shown to be linked to viral infections, since viruses are shed in extremely high numbers in the faeces and vomit of infected individuals and are routinely introduced into the water environment. All of the identified pathogenic viruses that pose a significant public health threat in the water environment are transmitted via the faecal-oral route. This group, are collectively known as enteric viruses, and their possible health effects include gastroenteritis, paralysis, meningitis, hepatitis, respiratory illness and diarrhoea. This review addresses both past and recent investigations into viral contamination of surface waters, with emphasis on six types of potential waterborne human pathogenic viruses. In addition, the viral associated illnesses are outlined with reference to their pathogenesis and routes of transmission.

Evaluation of four virus recovery methods for detecting noroviruses on fresh lettuce, sliced ham, and frozen raspberries

Although noroviruses play a significant role in causing foodborne illness in developed countries, no standardised method for detecting noroviruses in foodstuffs is currently available. This study compared four virus recovery methods based on ultrafiltration, immunomagnetic separation, ultracentrifugation and PEG precipitation techniques using identical real-time RT-PCR protocols for detection of RNA in eluates from lettuce, sliced ham and raspberries inoculated artificially with genogroup II norovirus. Noroviruses in all the food source matrices were successfully detected by all four methods. Ultracentrifugation yielded the highest recovery efficiencies in lettuce and ham, whereas PEG precipitation recovered the highest yield of noroviruses from raspberries. The repeatability of the results and the applicability of the methods to all food matrices were best with PEG precipitation, which had average virus recoveries of 19%, 47% and 28% for lettuce, ham and raspberries (viral RNA in dilution 1:10), respectively. In each case, a tenfold dilution of the extracted RNA clearly reduced the level of PCR inhibitors, which were released from raspberries in particular. The results of this study show that the detection of noroviruses in food is challenging, and more efforts to develop sensitive methods are still needed to detect noroviruses in food containing viruses in low numbers.

Surveillance of poliovirus circulation among refugees in Italy, 2008-2011

The aim of this study was to evaluate the presence of wild poliovirus or sabin-like poliovirus in 152 stool samples from migrants in the Accommodation Center in Italy and liquid waste from the sewage systems. Two surveys were performed in 2008 and 2011. All stool samples were negative for enterovirus and poliovirus. One of the liquid samples analyzed was positive for Coxsackievirus type B5.

Achievement V - Methods for breaking the transmission of pathogens along the food chain: Detection of viruses in food

Traditionally the focus for control of food-borne disease has been bacteria. During the last decade viruses have emerged as important sources of food borne human disease. Since the traditional bacteriological indicators, are not reliable for viral contamination, new methods are needed. PCR has enhanced the detection of virus in food. A challenge for developing detection reliable methods for viruses in food is that food matrices vary in composition, high sequence variability and inhibitors may be present. Therefore it is necessary to develop assays that have high diagnostic sensitivity, are broad and robust, and combine sample concentration and removal of inhibitors.

Detection of murine norovirus-1 by using TAT peptide-delivered molecular beacons

A TAT peptide-delivered molecular beacon was developed and utilized to enumerate murine norovirus 1, a human norovirus (NoV) surrogate, in RAW 264.7 cells. This allowed the detection of a single infective virus within 6 h, a 12-fold improvement in time required for viral detection and quantification compared to that required by the conventional plaque assay.

Amplification of viral RNA from drinking water using TransPlex™ whole-transcriptome amplification

Aims:  Viral pathogens in environmental media are generally highly diffuse, yet small quantities of pathogens may pose a health risk. This study evaluates the ability of TransPlex™ whole transcriptome amplification (WTA) to amplify small quantities of RNA viruses from complex environmental matrices containing background nucleic acids.

Methods and Results:  DNA extracts from mock drinking water samples containing mixed microbial populations were spiked with small quantities of echovirus type 13 (EV) RNA. Samples were amplified using a Transplex™ WTA kit, and EV‐specific quantitative reverse transcription polymerase chain reaction (qRT‐PCR) was used to quantify target pathogens before and after application of WTA. Samples amplified by WTA demonstrated a decreased limit of detection. The log‐linear relationship between serial dilutions was maintained following amplification by WTA.

Conclusions:  WTA is able to increase the quantity of target organism RNA in mixed populations, while maintaining log linearity of amplification across different target concentrations.

Significance and Impact of the Study:  WTA may serve as an effective preamplification step to increase the levels of RNA prior to detection by other molecular methods such as PCR, microarrays and sequencing.

Detection of rotavirus A in sewage samples using multiplex qPCR and an evaluation of the ultracentrifugation and adsorption-elution methods for virus concentration

Group A rotaviruses (RV-A) are the most common agents of viral gastroenteritis in children worldwide. The goal of this study was to compare two different methods to concentrate RV-A from sewage samples and to improve the detection and quantification of RV-A using a multiplex quantitative PCR assay with an internal control. Both RV-A and the internal control virus, bacteriophage PP7, were seeded into wastewater and then concentrated using either an ultrafiltration-based adsorption-elution protocol or an ultracentrifugation-based protocol. Real time multiplex quantitative PCR was used to quantify the purified RV-A and PP7, and the results of the multiplex assay were compared with the results of the monoplex assays. The ultracentrifugation-based method had a mean recovery rate of 47% (range: 34-60%), while the ultrafiltration-based adsorption-elution method had a mean recovery rate of 3.5% (range: 1.5-5.5%). These results demonstrate that ultracentrifugation is a more appropriate method for recovering RV-A from wastewater. This method together with the multiplex qPCR assay may be suitable for routine laboratory use.

Evaluation of various methods for recovering human norovirus and murine norovirus from vegetables and ham

We evaluated and optimized each step in an analytical method for detecting norovirus from various foods. We characterized the buffers needed for eluting norovirus from foods such as ham and lettuce. Two different concentration methods, polyethylene glycol (PEG) precipitation and hollow fiber ultrafiltration (HUF), were compared using both murine norovirus (MNV) and human norovirus (HuNoV). For PEG precipitation, an elution buffer containing 3% beef extract (pH 7.1) was more suitable than 0.05 M glycine plus 0.14 M NaCl (pH 7.5), and the recovery efficiency increased with increasing molecular weight of PEG. To determine the optimal buffer for concentrating norovirus by HUF, glycine buffers with different pH values and ionic strengths were examined as elution buffers. Overall, HUF was more efficient for norovirus recovery than was PEG precipitation. Because there was a significant positive correlation between MNV and HuNoV results, MNV could be a useful surrogate for detecting HuNoV in foods.

Development of an RNA extraction protocol for detection of waterborne viruses by reverse transcriptase quantitative PCR (RT-qPCR)

RNA extraction from environmental samples yields frequently an RNA preparation containing inhibitors of molecular reactions. Commercial RNA extraction kits commonly permit extraction of only 0.1-0.2 ml sample volume. An RNA extraction buffer (RNAX buffer) was formulated for the extraction of viral RNA from 4.0 ml using a silica column based protocol. To evaluate the RNAX buffer based protocol, we used hepatitis A virus (HAV) and coxsackievirus B3 (CVB3) to monitor the RNA extraction efficiency from environmental samples. For evaluation of viral RNA recovery from water concentrates which were prepared from river and pond water by PEG concentration, serial ten fold dilutions of two waterborne viruses were added to the water concentrates for evaluation by quantitative detection. Quantitative recovery of HAV and CVB3 was determined by reverse transcriptase quantitative real-time PCR (RT-qPCR). The extracted RNA was compatible with RT-qPCR and sensitivity of detection of 0.8PFU per reaction was found with RNAX buffer and the developed protocol. This level of sensitivity was obtained using viral RNA extracted from 4.0 ml of an inoculated water sample concentrate. The RNAX buffer developed in this study could be applicable to the detection of other pathogens in water and food.

Concentration of viruses from environmental waters using nanoalumina fiber filters

Human viral contamination in drinking and recreational water may persist for extensive periods of time and cause a significant health risk concern. The aim of this study is to evaluate a viral recovery method using a new electropositive charged nanoalumina filter and to compare results with the widely used negatively charged HAWP filter by Millipore Inc. The recovery of infectious recombinant adenovirus type 5 (rAd5) was tested using the Fluorescence-Activated Cell Sorting (FACS) assay, in parallel with viral genomes recovery assay by quantitative PCR (qPCR). The mean infectivity recoveries were 82-91% by nanoalumina filters eluted with 3% beef extract (BE, pH 6.0), and 78-90% by HAWP filters eluted with 3% BE (pH 9.0), respectively, from 1L of environmental samples seeded with 1 pfu/mL rAd5. The mean genome recoveries were 16-35% by nanoalumina filters eluted with BE (pH 6.0), and 29-66% by HAWP filters eluted with NaOH (pH 10.8) from different types of water, respectively. Water quality, concentration of viruses, filters, and elution buffers are factors that determine the viral recovery efficiencies. The nanoalumina filters also had higher filtration rates than HAWP filters for large volumes of environmental water samples (up to 10 L), thus, have an advantage in concentrating infectious viruses from environments without pre-filtration, adjusting pH or adding multivalent cations.

Improved detection of F-specific RNA coliphages in fecal material by extraction and polyethylene glycol precipitation

Male-specific RNA coliphages (F-RNA coliphages) have been proposed as a potential viral indicator of fecal contamination in water and foods because they are easy to culture and are a normal component of the mammalian gut flora. F-RNA coliphage plaque numbers are typically obtained by directly plating a 10-fold dilution of 1 g of fecal material, but the numbers of F-RNA coliphages shed by animals and humans may be too low for direct enumeration. Therefore, the sensitivity of detecting F-RNA coliphages in fecal material was improved by extracting and precipitating F-RNA coliphage from a 10-g fecal sample by use of polyethylene glycol (PEG). The highest recovery of F-RNA coliphage with 10% beef extract, pH 7.2, was obtained in the presence of 1 M NaCl and 10% PEG after 16 h of precipitation, but a pellet was not obtained after a short precipitation time of 2 h. There was no significant difference between eluant-to-fecal-material ratios of 4:1 and 9:1 or homogenization with a stomacher or pulsifier. F-RNA coliphage were detected in 64% (16 of 25 samples) of fecal samples from various sources when the sample size was 10 g but in 36% (9 of 25 samples) of samples when the sample size was 1 g. When F-RNA coliphage were detected in 1-g samples, they were also detected in 10-g samples. When F-RNA coliphage were detected in 10-g samples but not in 1-g samples, the levels were <100 PFU/g.

An analysis of water quality in the Colorado River, 2003-04; an investigation into recurring outbreaks of norovirus among rafters

BACKGROUND

Every year over 22 000 people raft the Colorado River through the Grand Canyon in Arizona. Since 1994, over 400 rafters in 6 separate outbreaks have become ill with norovirus while rafting this stretch of the river.

OBJECTIVES

To assess potential causes of these outbreaks, Colorado River water, water from nearby wastewater treatment plants, and a drinking water source were sampled and tested for norovirus and other water quality indicators.

METHODS

Colorado River water was collected and sampled during the 2004 rafting season. Water from wastewater treatment plants near the Lee's Ferry launch site and drinking water from the Lee's Ferry launch site were also examined during the 2003 and 2004 rafting seasons. Stool samples from ill rafters and composite stool samples from onboard toilet-cans were tested for the presence of norovirus during the 2003 and 2004 outbreaks. Parameters examined included the following: norovirus by reverse transcriptase- polymerase chain reaction, coliforms, Escherichia coli, temperature, turbidity, and pH.

RESULTS

No norovirus was detected in the Colorado River during the 2004 field sampling. Norovirus was detected in the Glen Canyon Dam Wastewater Treatment Plant on one occasion in 2004. Drinking water from the Lee's Ferry launch site was negative for norovirus in 2003, and Colorado River water from the Lee's Ferry launch site was negative for norovirus in 2004. In 2003, 3 of 10 stool samples from ill rafters or onboard toilet-cans were positive for norovirus. Neither of 2 stool samples collected in 2004 was positive for norovirus.

CONCLUSIONS

Colorado River water tested during nonoutbreak periods was negative for norovirus, indicating that there is not an ongoing high level of norovirus contamination in the river. No source or sources of contamination could be identified from the testing. Potential sources of norovirus outbreaks among rafters include drinking contaminated river water, consuming contaminated foodstuff, rafter importation of the virus and subsequent person-to-person spread, and contaminated fomites, campsites, or equipment. It is likely outbreaks are the result of more than one source of norovirus, and the exact source remains unknown for several outbreaks.

Long-term inactivation study of three enteroviruses in artificial surface and groundwaters, using PCR and cell culture

Since the transmission of pathogenic viruses via water is indistinguishable from the transmission via other routes and since the levels in drinking water, although significant for health, may be too low for detection, quantitative viral risk assessment is a useful tool for assessing disease risk due to consumption of drinking water. Quantitative viral risk assessment requires information concerning the ability of viruses detected in drinking water to infect their host. To obtain insight into the infectivity of viruses in relation to the presence of virus genomes, inactivation of three different enteroviruses in artificial ground and surface waters under different controlled pH, temperature, and salt conditions was studied by using both PCR and cell culture over time. In salt-peptone medium, the estimated ratio of RNA genomes to infectious poliovirus 1 in freshly prepared suspensions was about 10(0). At 4 degrees C this ratio was 10(3) after 600 days, and at 22 degrees C it was 10(4) after 200 days. For poliovirus 1 and 2 the RNA/infectious virus ratio was higher in artificial groundwater than in artificial surface water, but this was not the case for coxsackievirus B4. When molecular detection is used for virus enumeration, it is important that the fraction of infectious virus (based on all virus genomes detected) decays with time, especially at temperatures near 22 degrees C.

Inactivation of norovirus by chlorine disinfection of water

In an effort to validate previous research suggesting remarkable resistance of norovirus to free chlorine disinfection, we characterized the disinfection response of purified and dispersed Norwalk virus (NV) by bench-scale free chlorine disinfection using RT-PCR for virus assays. The inactivation of NV by two doses of free chlorine (1 and 5mg/L) at pH 6 and 5 degrees C based on two RT-PCR assays was similar to that of coliphage MS2, but much faster than that of poliovirus 1. Despite the underestimation of virus inactivation by RT-PCR assays, the predicted CT values for NV based on RT-PCR assays are lower than the ones for most other important waterborne viruses and the CT guidelines for chlorine disinfection of viruses under the Surface Water Treatment Rule by the United States Environmental Protection Agency. Overall, the results of this study indicate that NV is not highly resistant to free chlorine disinfection as suggested by previous research and it is likely that NV contamination of drinking water can be controlled by adequate free chlorine disinfection practices with provision of proper pre-treatment processes before chlorination.

Bioaccumulation, retention, and depuration of enteric viruses by Crassostrea virginica and Crassostrea ariakensis oysters

Crassostrea ariakensis oysters are under review for introduction into the Chesapeake Bay. However, the human health implications of the introduction have not been fully addressed. This study evaluated rates of bioaccumulation, retention, and depuration of viruses by Crassostrea virginica and C. ariakensis when the two oyster species were maintained in separate tanks containing synthetic seawater of various salinities (8, 12, or 20 ppt). Oyster bioaccumulation tanks were seeded with 10(3) PFU/ml of hepatitis A virus (HAV), poliovirus, male-specific bacteriophage (MS2), and murine norovirus 1 (MNV-1) and 10(3) PCR units/ml of human norovirus (NoV). After 24 h, depuration commenced as oysters (n = 255) were placed in pathogen-free seawater under continuous filtration. Oysters (n = 6) were sampled weekly for 1 month from each tank. Viral RNA was recovered using a modified proteinase K, guanidine, and glassmilk method and analyzed by quantitative reverse transcription-PCR. The odds of C. ariakensis oysters harboring NoV, MNV-1, or HAV were statistically greater than the odds of C. virginica oysters harboring the same viruses (MNV-1 odds ratio [OR], 4.5; P = 0.01; NoV OR, 8.4; P < 0.001; HAV OR, 11.4; P < 0.001). Unlike C. virginica, C. ariakensis bioaccumulated and retained NoV, MNV-1, and HAV for 1 month at all salinities. Additionally, the odds of an oyster testing positive for NoV was 25.5 times greater (P < 0.001) when the oyster also tested positive for MNV-1. This research helps assess the threat of C. ariakensis as a vehicle for viral pathogens due to the consumption of raw oysters and validates the role for MNV-1 as a surrogate for NoV.

One-year monthly quantitative survey of noroviruses, enteroviruses, and adenoviruses in wastewater collected from six plants in Japan

Sewerage systems are important nodes to monitor human enteric pathogens transmitted via water. A quantitative virus survey was performed once a month for a year to understand the seasonal profiles of noroviruses genotype 1 and genotype 2, enteroviruses, and adenoviruses in sewerage systems. A total of 72 samples of influent, secondary-treated wastewater before chlorination and effluent were collected from six wastewater treatment plants in Japan. Viruses were successfully recovered from 100ml of influent and 1000ml of the secondary-treated wastewater and effluent using the acid rinse method. Viruses were determined by the RT-PCR or PCR method to obtain the most probable number for each sample. All the samples were also assayed for fecal coliforms (FCs) by a double-layer method. The seasonal profiles of noroviruses genotype 1 and genotype 2 in influent were very similar, i.e. they were abundant in winter (from November to March) at a geometric mean value of 190 and 200 RT-PCR units/ml, respectively, and less frequent in summer (from June to September), at 4.9 and 9.1 RT-PCR units/ml, respectively. The concentrations of enteroviruses and adenoviruses were mostly constant all the year round, 17 RT-PCR units/ml and 320 PCR units/ml in influent, and 0.044 RT-PCR units/ml and 7.0 PCR units/ml in effluent, respectively.

Monitoring of waterborne pathogens in surface waters in amsterdam, the Netherlands, and the potential health risk associated with exposure to cryptosporidium and giardia in these waters

The water in the canals and some recreational lakes in Amsterdam is microbiologically contaminated through the discharge of raw sewage from houseboats, sewage effluent, and dog and bird feces. Exposure to these waters may have negative health effects. During two successive 1-year study periods, the water quality in two canals (2003 to 2004) and five recreational lakes (2004 to 2005) in Amsterdam was tested with regard to the presence of fecal indicators and waterborne pathogens. According to Bathing Water Directive 2006/7/EC, based on Escherichia coli and intestinal enterococcus counts, water quality in the canals was poor but was classified as excellent in the recreational lakes. Campylobacter, Salmonella, Cryptosporidium, and Giardia were detected in the canals, as was rotavirus, norovirus, and enterovirus RNA. Low numbers of Cryptosporidium oocysts and Giardia cysts were detected in the recreational lakes, despite compliance with European bathing water legislation. The estimated risk of infection with Cryptosporidium and Giardia per exposure event ranged from 0.0002 to 0.007% and 0.04 to 0.2%, respectively, for occupational divers professionally exposed to canal water. The estimated risk of infection at exposure to incidental peak concentrations of Cryptosporidium and Giardia may be up to 0.01% and 1%, respectively, for people who accidentally swallow larger volumes of the canal water than the divers. Low levels of viable waterborne pathogens, such as Cryptosporidium and Giardia, pose a possible health risk from occupational, accidental, and recreational exposure to surface waters in Amsterdam.

Evaluation of murine norovirus, feline calicivirus, poliovirus, and MS2 as surrogates for human norovirus in a model of viral persistence in surface water and groundwater

Human noroviruses (NoVs) are a significant cause of nonbacterial gastroenteritis worldwide, with contaminated drinking water a potential transmission route. The absence of a cell culture infectivity model for NoV necessitates the use of molecular methods and/or viral surrogate models amenable to cell culture to predict NoV inactivation. The NoV surrogates murine NoV (MNV), feline calicivirus (FCV), poliovirus (PV), and male-specific coliphage MS2, in conjunction with Norwalk virus (NV), were spiked into surface water samples (n = 9) and groundwater samples (n = 6). Viral persistence was monitored at 25 degrees C and 4 degrees C by periodically analyzing virus infectivity (for all surrogate viruses) and nucleic acid (NA) for all tested viruses. FCV infectivity reduction rates were significantly higher than those of the other surrogate viruses. Infectivity reduction rates were significantly higher than NA reduction rates at 25 degrees C (0.18 and 0.09 log(10)/day for FCV, 0.13 and 0.10 log(10)/day for PV, 0.12 and 0.06 log(10)/day for MS2, and 0.09 and 0.05 log(10)/day for MNV) but not significant at 4 degrees C. According to a multiple linear regression model, the NV NA reduction rates (0.04 +/- 0.01 log(10)/day) were not significantly different from the NA reduction rates of MS2 (0.05 +/- 0.03 log(10)/day) and MNV (0.04 +/- 0.03 log(10)/day) and were significantly different from those of FCV (0.08 +/- 0.03 log(10)/day) and PV (0.09 +/- 0.03 log(10)/day) at 25 degrees C. In conclusion, MNV shows great promise as a human NoV surrogate due to its genetic similarity and environmental stability. FCV was much less stable and thus questionable as an adequate surrogate for human NoVs in surface water and groundwater.

Detection of viral agents in fecal specimens of monkeys with diarrhea

BACKGROUND

Diarrheal disease is a major cause of morbidity and mortality in humans and animals, including non human primates. While the diagnostics for gastrointestinal bacterial and parasitic pathogens and their etiological role in disease are well established, little is known about the epidemiology, prevalence and role of viral agents in diarrheal illness among monkeys.

METHODS

We collected fecal specimens from monkeys with diarrhea that were housed in two primate colonies, the Institute of Laboratory Animal Sciences, Beijing, China and the Yerkes National Primate Research Center, Georgia, USA. We screened these fecal specimens for rotaviruses and enteric adenoviruses 40/41 by using commercial EIA kits (Rotaclone and Adenoclone), enteroviruses by RT-PCR and Southern blot hybridization, and picobirnaviruses by polyacrylamide gel electrophoresis and silver staining. Some of the specimens were examined by EM for coronaviruses and noroviruses.

RESULTS

Of the 92 specimens from China, we found 63 (68%) positive for viruses, including enteroviruses (52%), enteric adenoviruses (21%), rotaviruses (20%), and picobirnaviruses (2%). Coronaviruses were detected in some specimens. Mixed infection of two or more viral agents was seen in 23 (25%) specimens. In the US collection, we detected enteroviruses and enteric adenoviruses in 76% (45/59) and 14% (7/50) of the specimens, respectively. Electron microscopy showed norovirus-like particles in some specimens from both colonies.

CONCLUSIONS

Our findings indicate endemic infections with enteric viruses in monkeys of both colonies. The availability of new simian rotaviruses, enteric adenoviruses, enteroviruses, and coronaviruses and the discovery of noroviruses and picobirnaviruses may allow us to develop better diagnostics for these agents and determine which of these agents are clearly associated with gastroenteritis in monkeys.

The association between rainfall rate and occurrence of an enterovirus epidemic due to a contaminated well

AIMS

To determine the association between rainfall rate and occurrence of enterovirus infection related to contamination of drinking water.

METHODS AND RESULTS

One fatality case and three cases of severe illness were observed during the enterovirus epidemic in a village in southern Taiwan from 16 September to 3 October 1998. Groundwater samples were collected from the public well in the village after heavy rainfall to test for enterovirus using the reverse transcription-polymerase chain reaction (RT-PCR) assay. The RT-PCR assay detected the enterovirus in the groundwater sample collected on 26 September 1998. The logistic regression model also revealed a statistically significant association between the rainfall rate and the observation of cases of enterovirus infection.

CONCLUSIONS

According to the fitted logistic regression model, the probability of detecting cases of enterovirus infection was greater than 50% at rainfall rates >31 mm h(-1). The higher the rainfall rate, the higher the probability of enterovirus epidemic.

SIGNIFICANCE AND IMPACT OF THE STUDY

Contamination of drinking water by the enterovirus may lead to epidemics that cause deaths and severe illness, and such contamination may be caused by heavy rainfall. The major finding in this study is that the enterovirus could be flushed to groundwater in an unconfined aquifer after a heavy rainfall. This work allows for a warning level so that an action can be taken to minimize future outbreaks and so protect public health.