Electropositive filter membrane as an alternative for the elimination of PCR inhibitors from sewage and water samples

Occurrence of norovirus genogroups I and II in recreational water from four beaches in Belém city, Brazilian Amazon region

This study aimed to investigate the presence of norovirus (NoV) in recreational waters of four estuarine beaches located in Mosqueiro Island, Belém city, Brazilian Amazon, during two years of monitoring (2012 and 2013). NoV particles were concentrated on filtering membrane by the adsorption-elution method and detected by semi-nested RT-PCR (reverse transcription polymerase chain reaction) and sequencing. NoV positivity was observed in 37.5% (39/104) of the surface water samples, with genogroup GI (69.2%) occurring at a higher frequency than GII (25.7%), with a cocirculation of both genogroups in two samples (5.1%). This virus was detected in all sampling points analyzed, showing the highest detection rate at the Paraíso Beach (46.2%). Statistically, there was a dependence relationship between tide levels and positive detection, with a higher frequency at high tide (46.7%) than at low tide (25%) periods. Months with the highest detection rates (April 2012 and April/May 2013) were preceded by periods of higher precipitation (March 2012 and February/March 2013). Phylogenetic analysis showed the circulation of the old pandemic variant (GII.4-US_95-96) and GI.8. The NoV detection demonstrated viral contamination on the beaches and evidenced the health risk to bathers, mainly through recreational activities such as bathing, and highlighted the importance of including enteric viruses research in the recreational water quality monitoring.

Evaluation of Well Designs to Improve Access to Safe and Clean Water in Rural Tanzania

The objective of this study was to examine three well designs: drilled wells (20–30 m deep), closed dug wells (>5 m deep), and hand-dug open wells (<5 m deep), to determine the water quality for improving access to safe and clean water in rural communities. Heterotrophic plate count (HPC), total coliforms (TC), Escherichia coli (E. coli) and turbidity, were used to assess the water quality of 97 wells. Additionally, the study looked at the microflora diversity of the water, focusing on potential pathogens using outgrowth, PCR, and genome sequencing for 10 wells. Concentrations of TC for the open dug wells (4 × 10⁴ CFU/100 mL) were higher than the drilled (2 × 10³ CFU/100 mL) and closed dug wells (3 × 10³ CFU/100 mL). E. coli concentration for drilled and closed dug wells was <22 MPN (most probable number)/100 mL, but higher for open wells (>154 MPN/100 mL). The drilled well turbidity (11 NTU) was within the standard deviation of the closed well (28 NTU) compared to open dug wells (49 NTU). Drilled and closed wells had similar microbial diversity. There were no significant differences between drilled and closed dug wells. The covering and lining of hand-dug wells should be considered as an alternative to improve access to safe and clean water in rural communities.

Identification of circo-like virus-Brazil genomic sequences in raw sewage from the metropolitan area of São Paulo: evidence of circulation two and three years after the first detection

BACKGROUND

Two novel viruses named circo-like virus-Brazil (CLV-BR) hs1 and hs2 were previously discovered in a Brazilian human fecal sample through metagenomics. CLV-BR hs1 and hs2 possess a small circular DNA genome encoding a replication initiator protein (Rep), and the two genomes exhibit 92% nucleotide identity with each other. Phylogenetic analysis based on the Rep protein showed that CLV-BRs do not cluster with circoviruses, nanoviruses, geminiviruses or cycloviruses.

OBJECTIVE

The aim of this study was to search for CLV-BR genomes in sewage and reclaimed water samples from the metropolitan area of São Paulo, Brazil, to verify whether the first detection of these viruses was an isolated finding.

METHODS

Sewage and reclaimed water samples collected concomitantly during the years 2005-2006 were purified and concentrated using methodologies designed for the study of viruses. A total of 177 treated reclaimed water samples were grouped into five pools, as were 177 treated raw sewage samples. Nucleic acid extraction, polymerase chain reaction (PCR) amplification and Sanger sequencing were then performed.e.

FINDINGS CLV-BR

genomes were detected in two pools of sewage samples, p6 and p9. Approximately 28% and 51% of the CLV-BR genome was amplified from p6 and p9, respectively, including 76% of the Rep gene. The detected genomes are most likely related to CLV-BR hs1. Comparative analysis showed several synonymous substitutions within Rep-encoding sequences, suggesting purifying selection for this gene, as has been observed for other eukaryotic circular Rep-encoding single-stranded DNA (CRESS-DNA) viruses.

MAIN CONCLUSION

The results therefore indicated that CLV-BR has continued to circulate in Brazil two and three years after first being detected.

GenSeed-HMM: A Tool for Progressive Assembly Using Profile HMMs as Seeds and its Application in Alpavirinae Viral Discovery from Metagenomic Data

This work reports the development of GenSeed-HMM, a program that implements seed-driven progressive assembly, an approach to reconstruct specific sequences from unassembled data, starting from short nucleotide or protein seed sequences or profile Hidden Markov Models (HMM). The program can use any one of a number of sequence assemblers. Assembly is performed in multiple steps and relatively few reads are used in each cycle, consequently the program demands low computational resources. As a proof-of-concept and to demonstrate the power of HMM-driven progressive assemblies, GenSeed-HMM was applied to metagenomic datasets in the search for diverse ssDNA bacteriophages from the recently described Alpavirinae subfamily. Profile HMMs were built using Alpavirinae-specific regions from multiple sequence alignments (MSA) using either the viral protein 1 (VP1; major capsid protein) or VP4 (genome replication initiation protein). These profile HMMs were used by GenSeed-HMM (running Newbler assembler) as seeds to reconstruct viral genomes from sequencing datasets of human fecal samples. All contigs obtained were annotated and taxonomically classified using similarity searches and phylogenetic analyses. The most specific profile HMM seed enabled the reconstruction of 45 partial or complete Alpavirinae genomic sequences. A comparison with conventional (global) assembly of the same original dataset, using Newbler in a standalone execution, revealed that GenSeed-HMM outperformed global genomic assembly in several metrics employed. This approach is capable of detecting organisms that have not been used in the construction of the profile HMM, which opens up the possibility of diagnosing novel viruses, without previous specific information, constituting a de novo diagnosis. Additional applications include, but are not limited to, the specific assembly of extrachromosomal elements such as plastid and mitochondrial genomes from metagenomic data. Profile HMM seeds can also be used to reconstruct specific protein coding genes for gene diversity studies, and to determine all possible gene variants present in a metagenomic sample. Such surveys could be useful to detect the emergence of drug-resistance variants in sensitive environments such as hospitals and animal production facilities, where antibiotics are regularly used. Finally, GenSeed-HMM can be used as an adjunct for gap closure on assembly finishing projects, by using multiple contig ends as anchored seeds.

Measuring and mitigating inhibition during quantitative real time PCR analysis of viral nucleic acid extracts from large-volume environmental water samples

Naturally-occurring inhibitory compounds are a major concern during qPCR and RT-qPCR analysis of environmental samples, particularly large volume water samples. Here, a standardized method for measuring and mitigating sample inhibition in environmental water concentrates is described. Specifically, the method 1) employs a commercially available standard RNA control; 2) defines inhibition by the change in the quantification cycle (C(q)) of the standard RNA control when added to the sample concentrate; and 3) calculates a dilution factor using a mathematical formula applied to the change in C(q) to indicate the specific volume of nuclease-free water necessary to dilute the effect of inhibitors. The standardized inhibition method was applied to 3,193 large-volume water (surface, groundwater, drinking water, agricultural runoff, sewage) concentrates of which 1,074 (34%) were inhibited. Inhibition level was not related to sample volume. Samples collected from the same locations over a one to two year period had widely variable inhibition levels. The proportion of samples that could have been reported as false negatives if inhibition had not been mitigated was between 0.3% and 71%, depending on water source. These findings emphasize the importance of measuring and mitigating inhibition when reporting qPCR results for viral pathogens in environmental waters to minimize the likelihood of reporting false negatives and under-quantifying virus concentration.

PCR inhibitors - occurrence, properties and removal

The polymerase chain reaction (PCR) is increasingly used as the standard method for detection and characterization of microorganisms and genetic markers in a variety of sample types. However, the method is prone to inhibiting substances, which may be present in the analysed sample and which may affect the sensitivity of the assay or even lead to false-negative results. The PCR inhibitors represent a diverse group of substances with different properties and mechanisms of action. Some of them are predominantly found in specific types of samples thus necessitating matrix-specific protocols for preparation of nucleic acids before PCR. A variety of protocols have been developed to remove the PCR inhibitors. This review focuses on the general properties of PCR inhibitors and their occurrence in specific matrices. Strategies for their removal from the sample and for quality control by assessing their influence on the individual PCR test are presented and discussed.

Rapid detection method for hepatitis A virus from lettuce by a combination of filtration and integrated cell culture-real-time reverse transcription PCR

We have developed a rapid and simple method for filtration using a positively charged membrane to concentrate hepatitis A virus (HAV) from lettuce and an integrated cell culture-real-time reverse transcription PCR (ICC-real-time RT-PCR) to detect infectious HAV. The most suitable buffer for HAV concentration by filtration was 100 mM Tris-HCl, 50 mM glycine (pH 9.5). Filtration using the NanoCeram matrix was compared with polyethylene glycol precipitation for viral concentration from lettuce inoculated with 6 log RNA copies of HAV. The recovery rate of filtration was statistically higher than that of polyethylene glycol precipitation (47.3 versus 24.9%, respectively). The sensitivity of ICC-real-time RT-PCR for detection of infectious HAV was determined by inoculation of FRhK-4 cells with HAV (4 log to 0 log RNA copies). ICC-real-time RT-PCR detected infectious HAV on average 5 days earlier than cytopathic effects at all inoculation levels. HAV recovered from lettuce (approximately 3 log RNA copies) was also analyzed with ICC-real-time RT-PCR. Infectious HAV was detected within 2 days postinfection by ICC-real-time RT-PCR, whereas cytopathic effects were not observed until 7 days postinfection. Coupled with a virus concentration and purification system using a positively charged membrane, ICC-real-time RT-PCR has the potential to become a novel and rapid method for the detection of infectious HAV in vegetables.

Phylodynamics and movement of Phycodnaviruses among aquatic environments

Phycodnaviruses have a significant role in modulating the dynamics of phytoplankton, thereby influencing community structure and succession, nutrient cycles and potentially atmospheric composition because phytoplankton fix about half the carbon dioxide (CO(2)) on the planet, and some algae release dimethylsulphoniopropionate when lysed by viruses. Despite their ecological importance and widespread distribution, relatively little is known about the evolutionary history, phylogenetic relationships and phylodynamics of the Phycodnaviruses from freshwater environments. Herein we provide novel data on Phycodnaviruses from the largest river system on earth--the Amazon Basin--that were compared with samples from different aquatic systems from several places around the world. Based on phylogenetic inference using DNA polymerase (pol) sequences we show the presence of distinct populations of Phycodnaviridae. Preliminary coarse-grained phylodynamics and phylogeographic inferences revealed a complex dynamics characterized by long-term fluctuations in viral population sizes, with a remarkable worldwide reduction of the effective population around 400 thousand years before the present (KYBP), followed by a recovery near to the present time. Moreover, we present evidence for significant viral gene flow between freshwater environments, but crucially almost none between freshwater and marine environments.

Mycobacterium behavior in wastewater treatment plant, a bacterial model distinct from Escherichia coli and Enterococci

Mycobacteria are waterborne emerging pathogens causing infections in human. Mycobacteria have been previously isolated from wastewater and sludge, but their densities were not estimated due to cultural biases. In order to evaluate the impact of wastewater treatment processes on mycobacteria removal, we used a real time PCR method. First we compared six DNA extraction methods and second we used the more efficient DNA extraction procedure (i.e., enzymatic lysis combined with hexadecyltrimethylammonium bromide-NaCl procedure) in order to quantify Mycobacterium. With the aim to identify parameters that could serve as indicator of mycobacterial behavior, mycobacterial densities were measured in parallel to those of Escherichia coli and enterococci, and to concentrations of chemical parameters usually monitored in wastewater. Mycobacterium reached 5.5 × 10⁵ ± 3.9 × 10⁵ copies/L in the influent, but was not detected in the effluent after decantation and biofiltration. Most mycobacteria (98.6 ± 2.7%, i.e. 2.4 ± 0.7 log₁₀) were removed by the physical-chemical decantation, and the remaining mycobacteria were removed by biofiltration. In contrast, enterococci and E. coli were lightly removed by decantation step and mainly removed by biofiltration. Our results showed that Mycobacterium corresponds to a hydrophobic behavior linked to insoluble compound removal, whereas enterococci and E. coli refer to hydrophilic behaviors linked to soluble compound removals.

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.

Comparison of different concentration methods for the detection of hepatitis A virus and calicivirus from bottled natural mineral waters

Viral contamination of drinking water is frequently reported as the primary source of gastroenteritis or hepatitis outbreaks. The presence of viruses at low concentration levels in most environmental water poses major analytical problems when determining their concentration. To evaluate the efficiency of different recovery methods of viral RNA from bottled water, a comparison was made of 2 positively and 2 negatively charged membranes that were used for absorbing and releasing HAV virus particles during the filtration of viral spiked bottled water. All the 4 membranes, regardless of charge and pore size, had low level viral recovery. The results show that a considerable number of the virus particles passed through the pores of the membranes instead of being trapped by the electrostatic charges. Two different procedures were then compared using 1.5L polyethylene bottles spiked with 10-fold serial dilutions of HAV and FCV. The first procedure included an ultrafiltration-based method followed by MiniMag RNA extraction, and the second an ultracentrifugation-based method followed by RNA extraction using QIAamp viral RNA mini kit. The ultracentrifugation-based method resulted in a better recovery of HAV and FCV when compared to the ultrafiltration-based method.

Hepatitis E virus-based evaluation of a virion concentration method and detection of enteric viruses in environmental samples by multiplex nested RT-PCR

AIMS

The prevalence of enteric viruses in drinking and river water samples collected from Pune, India was assessed. During an outbreak of HEV in a small town near pune, water samples were screened for enteric viruses.

METHODS AND RESULTS

The water samples were subjected to adsorption-elution-based virus concentration protocol followed by multiplex nested PCR. Among 64 Mutha river samples, 49 (76.56%) were positive for Hepatitis A Virus, 36 (56.25%) were positive for Rotavirus, 33 (51.56%) were positive for Enterovirus and 16 (25%) were positive for Hepatitis E Virus RNA. Only enterovirus RNA was detected in 2/662 (0.3%) drinking water samples, and the samples from the city's water reservoir tested negative for all four viruses. HEV RNA was detected in three out of four river water samples during HEV outbreak and partial sequences from patients and water sample were identical.

CONCLUSIONS

The study suggests absence of enteric viruses both in the source and in the purified water samples from Pune city, not allowing evaluation of the purification system and documents high prevalence of enteric viruses in river water, posing threat to the community.

SIGNIFICANCE AND IMPACT OF THE STUDY

The rapid, sensitive and relatively inexpensive protocol developed for virological evaluation of water seems extremely useful and should be adapted for evaluating viral contamination of water for human consumption. This will lead to development of adequate control measures thereby reducing disease burden because of enteric viruses.

Development of monoclonal antibody-coated immunomagnetic beads for separation and detection of norovirus (genogroup II) in faecal extract samples

AIMS

The aim of this study is to develop an RT-PCR assay combined with immunomagnetic beads (IMS/RT-PCR) coating monoclonal antibody (Mab) for separation and detection of norovirus (genogroup II) in faecal samples. We furthermore compare its detection limits with IMS/RT-PCR using polyclonal antibody (Pab) and the TRIzol extraction method followed by RT-PCR (TRIzol-RT-PCR).

METHODS AND RESULTS

Mab-coated beads and Pab-coated beads were added to a series of tenfold dilutions of faecal extract containing norovirus in 1 ml PBS. After incubation and collection, the RNA was released by heating from virus separated by beads. The tenfold dilutions of faecal were also extracted with TRIzol reagent. The RNA was used as the template for RT-PCR detection (primers: JV12-JV13). IMS/RT-PCR using Mab showed an endpoint in the 10(-7) dilution and was 10(2) times more sensitive than IMS/RT-PCR using Pab and was at least 10(3) times more sensitive than TRIzol-RT-PCR method.

CONCLUSIONS

IMS/RT-PCR using Mab proved to be a more sensitive method of noroviruses (NVs) detection than IMS/RT-PCR using Pab and the TRIzol-RT-PCR method.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first study to detect NVs with IMS/RT-PCR using Mab, and could serve as a model for future assays when broadly reactive NVs-specific Mabs are developed.

Longitudinal study on occurrence of adenoviruses and hepatitis A virus in raw domestic sewage in the city of Limeira, SÃo Paulo

The aim of this study was to verify the presence and annual distribution of adenoviruses and hepatitis A virus in domestic sewage in the city of Limeira, São Paulo. Fifty samples with a volume of 8 liters each were collected weekly from December 2004 to December 2005. The viruses were concentrated by filtration through positively charged ZP60S filter membranes, followed by ultracentrifugation. Human adenoviruses (HAdV) were detected by PCR followed by nested-PCR and screening for species F was done by restriction of the PCR product with TaqI endonuclease. Virus infectivity assays were performed by inoculation of concentrates onto HEp-2 cell monolayers. RT-PCR was used for the detection of hepatitis A virus. HAdV were detected in all samples, and 64% of samples were positive for infectious virus. Species F was present in 82% of the samples. Hepatitis A virus was detected in 48% of the samples. These results demonstrate that HAdV and HAV were present in the domestic sewage of Limeira throughout the period of study, demonstrating the importance of an adequate treatment before the disposal in the environment.

Development of sample storage methods for detecting enteric viruses in environmental water

In a field survey of enteric viruses, water samples collected sometimes need to be stored for a long duration before analysis is performed. The aim of this study was to develop an appropriate sample storage method for detecting viruses in environmental water. Three types of sample storage methods were evaluated using MilliQ water, pond water, and treated sewage inoculated with poliovirus and norovirus: (i) storage followed by the full concentration procedure, (ii) filtration and storage followed by the remaining concentration procedure, and (iii) the full concentration procedure before storage. The recovery of norovirus on day 0 of inoculation was 110.2+/-38.2% (n=2), which was comparable to that of poliovirus. During sample storage for up to 13 days, virus recovery showed different patterns of decrease, depending on the storage method, sample type, and storage temperature. Among the three methods tested, the method of storing the eluted samples was judged to be most appropriate for detection of viruses from water samples. This method does not require any special equipment and can be easily adopted in field surveys, especially in developing countries.

Molecular identification and genetic analysis of Norovirus genogroups I and II in water environments: comparative analysis of different reverse transcription-PCR assays

Noroviruses have received increased attention in recent years because their role as etiologic agents in acute gastroenteritis outbreaks is now clearly established. Our inability to grow them in cell culture and the lack of an animal model hinder the characterization of these viruses. More recently, molecular approaches have been used to study the genetic relationships that exist among them. In the present study, environmental samples from seawater, estuarine water, and effluents of sewage treatment plants were analyzed in order to evaluate the role of environmental surface contamination as a possible vehicle for transmission of norovirus genogroups I and II. Novel broad-range reverse transcription-PCR/nested assays targeting the region coding for the RNA-dependent RNA polymerase were developed, amplifying fragments of 516 bp and 687 bp in the nested reactions for genogroups II and I, respectively. The assays were evaluated and compared against widely used published assays. The newly designed assays provide long regions for high-confidence BLAST searches in public databases and therefore are useful diagnostic tools for molecular diagnosis and typing of human noroviruses in clinical and environmental samples, as well as for the study of molecular epidemiology and the evolution of these viruses.

Use of TaqMan real-time reverse transcription-PCR for rapid detection, quantification, and typing of norovirus

Noroviruses (NoVs) are the most commonly identified cause of outbreaks and sporadic cases of acute gastroenteritis. We evaluated and optimized NoV-specific TaqMan real-time reverse transcription (RT)-PCR assays for the rapid detection and typing of NoV strains belonging to genogroups GI and GII and adapted them to the LightCycler platform. We expanded the detection ability of the assays by developing an assay that detects the GIV NoV strain. The assays were validated with 92 clinical samples and 33 water samples from confirmed NoV outbreaks and suspected NoV contamination cases. The assays detected NoV RNA in all of the clinical specimens previously confirmed positive by conventional RT-PCR and sequencing. Additionally, the TaqMan assays successfully detected NoV RNA in water samples containing low viral concentrations and inhibitors of RT and/or PCR, whereas the conventional method with region B primers required dilution of the inhibitors. By means of serially diluted NoV T7 RNA transcripts, a potential detection limit of <10 transcript copies per reaction mixture was observed with the GII assay and a potential detection limit of <100 transcript copies per reaction mixture was observed with the GI assay. These results and the ability to detect virus in water that was negative by RT-PCR demonstrate the higher sensitivity of the TaqMan assay compared with that of a conventional RT-PCR assay. The TaqMan methods dramatically decrease the turnaround time by eliminating post-PCR processing. These assays have proven useful in assisting scientists in public health and diagnostic laboratories report findings quickly to outbreak management teams.

High throughput screening for spores and vegetative forms of pathogenic B. anthracis by an internally controlled real-time PCR assay with automated DNA preparation

Human infections with Bacillus anthracis have become rare but in cases of intentional release, masses of samples would have to be expected. Current PCR assays for anthrax are appropriate for use in single cases, but they have not been formulated for high throughput screening. This article describes a high throughput real-time PCR for anthrax, including automated sample preparation without the need for pre-culturing of samples. The assay detects single copies of target gene. An internal control monitors the whole assay including sample preparation. The limit of detection in blood was 1,066 (95%CI, 741-1,739) copies/ml, corresponding to 4.4-32.3 organisms/ml. Using spore preparations, 20 colony-forming units (CFU) per sample could be detected reliably (0.8 CFU per PCR). The extraction procedures depleted viable spores from solution by factors of 10,000 (automated procedure) and >100,000 (conventional column procedure). One hundred and ten clinical and environmental specimens were retested, 50 of them sampled during a period of heightened anthrax awareness in 2001. A widely used assay yielded two false positive results (cross-reaction with B. cereus), while the new assay tested all samples negative. The internal control operated stable in all clinical samples. The assay is capable of testing for anthrax in the high throughput mode.

Detection of norovirus capsid protein in authentic standards and in stool extracts by matrix-assisted laser desorption ionization and nanospray mass spectrometry

Mass spectrometry (MS) represents a rapid technique for the identification of microbial monocultures, and its adaptation to the detection of pathogens in real-world samples is a public health and homeland security priority. Norovirus, a leading cause of gastroenteritis in the world, is difficult to monitor because it cannot be cultured outside the human body. The detection of norovirus capsid protein was explored using three common MS-based methods: scanning of intact proteins, peptide mass fingerprinting, and peptide sequencing. Detection of intact target protein was limited by poor selectivity and sensitivity. Detection of up to 16 target peptides by peptide mass fingerprinting allowed for the reproducible and confident (P < 0.05) detection of the 56-kDa norovirus capsid protein in the range of 0.1 x 10(-12) to 50 x 10(-12) mol in authentic standards of recombinant norovirus virus-like particles (VLPs). To explore assay performance in complex matrixes, a non-gel-based, rapid method (2 to 3 h) for virus extraction from human stool was evaluated (72% +/- 12% recovery), and additional analyses were performed on norovirus-free stool extracts fortified with VLPs. Whereas peptide mass fingerprinting was rendered impractical by sample interferences, peptide sequencing using nanospray tandem MS facilitated unambiguous identification of > or =250 fmol of capsid protein in stool extracts. This is the first report on MS-based detection of norovirus, accomplished by using structurally identical, noninfective VLPs at clinically relevant concentrations. It represents an important milestone in the development of assays for surveillance of this category B bioterrorism agent.

Comparative study of four extraction methods for enterovirus recovery from wastewater and sewage sludge

This study investigated four methods for the recovery of enteroviruses from sterilized raw wastewater, activated sludge, thickened sludge and treated wastewater, inoculated with Echovirus 11, Gregory prototype. The adsorption-elution method recommended by the US Environmental Protection Agency (EPA) was better for Echovirus 11 recovery than a sonication method, a modified EPA method and a membrane adsorption elution method since it resulted in the highest detection levels by cell culture and RT-PCR (Friedman's test, p<0.00041 and p=0.041, respectively).

Concentration and detection of hepatitis A virus and rotavirus in spring water samples by reverse transcription-PCR

Every year, enteric viruses such as hepatitis A virus (HAV), rotaviruses, and noroviruses are responsible for viral gastro-enteritis and hepatitis reported worldwide. These viruses are mostly transmitted via the faecal-oral route, from direct contact between people, or by ingestion of contaminated food and water. Since only a few viral particles may cause disease, detection of low concentration of these viruses in food matrices is usually complex. The development of methods to concentrate viruses from food matrices is crucial in collecting data for the development of control strategies or for diagnostic purposes. In the present study, samples of bottled spring water were inoculated with known amounts of HAV (strain HM-175), and rotaviruses (strain Wa) viral particles and filtered through positively charged membranes. Elution of viruses attached to the membranes was achieved with a tryptose phosphate broth-glycine buffer. Eluates were further concentrated using Microsep 100. Finally, RNA was extracted using the Qiagen RNeasy kit followed by an evaporation step with a SpeedVac instrument. The detection limit by reverse-transcription (RT-PCR) was at least 10(-1) TCID50%/ml and at least 10(-3) TCID50%/ml for HAV and rotavirus, respectively.

An efficient virus concentration method and RT-nested PCR for detection of rotaviruses in environmental water samples

Water samples were concentrated by the modified adsorption-elution technique followed by speedVac reconcentration of the filter eluates. Reverse transcriptase-nested polymerase chain reaction (RT-nested PCR) was used to detect rotavirus RNA in concentrates of the water. The detection limit of the rotavirus determined by RT-nested PCR alone was about 1.67 plaque forming units (PFU) per RT-PCR assay and that by RT-nested PCR combined with concentration from 1l seeded tap water sample was 1.46 plaque forming units per assay. Water samples were collected from various sources, concentrated, and determined rotavirus RNA. Of 120 water samples, rotavirus RNA was detected in 20 samples (16.7%); 2/10 (20%) of the river samples, 8/30 (26.7%) of the canal samples, and 10/40 (25%) of the sewage samples but was not found in any tap water samples (0/40). Only three water samples were positive for rotavirus antigen determined using an enzyme-linked immunosorbent assay (ELISA). Alignment analysis of the sequenced PCR product (346-bp fragment) was performed in eight rotavirus-positive samples using the rotavirus sequence deposited in the GenBank. All samples gave the correct VP7 sequence. Results of analysis showed two samples similar to human rotavirus (97-98%), five similar to rotavirus G9 sequence (94-99%), and one sample similar to animal rotavirus (97%). PCR inhibitors were not observed in any concentrated water samples. In all 20 (of 120) samples where rotaviruses were found, fecal coliforms including Escherichia coli were also found, but of the samples testing negative for rotaviruses, 76 were fecal coliforms positive and 69 were E. coli positive. The combination of the virus concentration method and RT-nested PCR described below made it possible to effectively detect rotaviruses in environmental water samples.

A SYBR green, real-time RT-PCR method to detect and quantitate Norwalk virus in stools

A simple, single tube, hot start, real-time reverse transcription-PCR (rt RT-PCR) technique using SYBR green fluorescence was developed for the detection of genogroup I, cluster 1 Norwalk virus (NV) in stools. Sample dilution and heat release of viral RNA was effective as an alternative to more complex procedures to extract viruses from stool specimens. Real-time RT-PCR was applied to 68 stool isolates from patients participating in a NV volunteer study. First derivative melt curves were used to verify NV amplicon and to rule out the presence of primer dimer or spurious product. A dilution end-point standard curve was developed to semi-quantitate minimum virus levels and the results showed the number of RT-PCR amplifiable NV as high as 6.16 x 10(10)g(-1) of stool. The application of these methods was instrumental in identifying three asymptomatic patients who shed viruses in their stools, thus demonstrating a carrier state among seemingly healthy individuals. This study serves as a model for the development of rapid and specific detection, verification, and quantitation procedures for other Noroviruses in stools.

Monitoring bacterial pathogens in the environment: advantages of a multilayered approach

The application of advanced and highly sensitive molecular techniques to the detection of specific bacteria in the freshwater environment is limited, in the first instance, by sampling strategy and sample quality. Further combinations of molecular methods and techniques from apparently unrelated disciplines will ultimately shape the monitoring techniques of the future.