Processing and transport of environmental virus samples

CRISPR/Cas13a combined with reverse transcription and RPA for NoV GII.4 monitoring in water environments

Water bodies contaminated with the norovirus (NoV) are important vectors for its transmission. Therefore, enhanced monitoring of NoV in aqueous environments plays an active role in preventing diseases. Here, we reverse transcribed viral RNA into cDNA, and then used the constructed RPA-CRISPR/Cas13a-based platform for sensitive and quantitative monitoring of NoV GII.4 in aqueous environments. The use of glycerol as a phase separator and the direct release of nucleic acids from the virus by NaOH significantly enhanced the stability of the assay and reduced its economic cost. This assay is sensitive, specific, and stable. Based on the qualitative detection method, we established a relatively accurate quantitative detection method using the plasmid as a standard. Four water samples, totaling 64 samples, were analyzed using this method and compared with the qPCR method. The results of the two methods showed 100 % concordance with no significant difference in viral load. The entire process of our established method-from viral nucleic acid extraction to the output of the results-was completed in 30 min, much less than the time required for qPCR method. This suggests that the assay can be used as an alternative to qPCR for monitoring the change of NoV GII.4 concentration in water bodies, and shows high potential for application in the immediate detection of viruses in aqueous environments and resource-limited areas.

Applicability of integrated cell culture reverse transcriptase quantitative PCR (ICC-RTqPCR) for the simultaneous detection of the four human enteric enterovirus species in disinfection studies

A newly developed integrated cell culture reverse transcriptase quantitative PCR (ICC-RTqPCR) method and its applicability in UV disinfection studies is described. This method utilizes a cell culture system coupled with four RTqPCR assays to detect four species of human enterovirus (e.g., Enterovirus A, Enterovirus B, Enterovirus C and Enterovirus D). Evaluation of the RTqPCR assays was conducted with coxsackievirus A10, echovirus 30, poliovirus 1 and enterovirus 70 and resulted in 100% specificity for the tested assays. A comparison of ICC-RTqPCR between the individual enteroviruses and a mixture of all four viruses resulted in an approximate 1:1 correlation, demonstrating a lack of competition during incubation in cell culture and RTqPCR. The simultaneous detection of multiple human enterovirus species within mixed cultures is relevant to many applications, including virus disinfection studies. This high-throughput, multiplex approach costs less in money and time. By helping with data collection, this approach will lead to more statistically sound data sets that directly compare the inactivation rates of enteroviruses tested.

Virus hazards from food, water and other contaminated environments

Numerous viruses of human or animal origin can spread in the environment and infect people via water and food, mostly through ingestion and occasionally through skin contact. These viruses are released into the environment by various routes including water run-offs and aerosols. Furthermore, zoonotic viruses may infect humans exposed to contaminated surface waters. Foodstuffs of animal origin can be contaminated, and their consumption may cause human infection if the viruses are not inactivated during food processing. Molecular epidemiology and surveillance of environmental samples are necessary to elucidate the public health hazards associated with exposure to environmental viruses. Whereas monitoring of viral nucleic acids by PCR methods is relatively straightforward and well documented, detection of infectious virus particles is technically more demanding and not always possible (e.g. human norovirus or hepatitis E virus). The human pathogenic viruses that are most relevant in this context are nonenveloped and belong to the families of the Caliciviridae, Adenoviridae, Hepeviridae, Picornaviridae and Reoviridae. Sampling methods and strategies, first-choice detection methods and evaluation criteria are reviewed.

Virus hazards from food, water and other contaminated environments

Numerous viruses of human or animal origin can spread in the environment and infect people via water and food, mostly through ingestion and occasionally through skin contact. These viruses are released into the environment by various routes including water run-offs and aerosols. Furthermore, zoonotic viruses may infect humans exposed to contaminated surface waters. Foodstuffs of animal origin can be contaminated, and their consumption may cause human infection if the viruses are not inactivated during food processing. Molecular epidemiology and surveillance of environmental samples are necessary to elucidate the public health hazards associated with exposure to environmental viruses. Whereas monitoring of viral nucleic acids by PCR methods is relatively straightforward and well documented, detection of infectious virus particles is technically more demanding and not always possible (e.g. human norovirus or hepatitis E virus). The human pathogenic viruses that are most relevant in this context are nonenveloped and belong to the families of the Caliciviridae, Adenoviridae, Hepeviridae, Picornaviridae and Reoviridae. Sampling methods and strategies, first-choice detection methods and evaluation criteria are reviewed.

New electropositive filter for concentrating enteroviruses and noroviruses from large volumes of water

The U.S. Environmental Protection Agency's information collection rule requires the use of 1MDS electropositive filters for concentrating enteric viruses from water, but unfortunately, these filters are not cost-effective for routine viral monitoring. In this study, an inexpensive electropositive cartridge filter, the NanoCeram filter, was evaluated for its ability to concentrate enteroviruses and noroviruses from large volumes of water. Seeded viruses were concentrated using the adsorption-elution procedure. The mean percent retention of seeded polioviruses by NanoCeram filters was 84%. To optimize the elution procedure, six protocols, each comprising two successive elutions with various lengths of filter immersion, were evaluated. The highest virus recovery (77%) was obtained by immersing the filters in beef extract for 1 minute during the first elution and for 15 min during the second elution. The recovery efficiencies of poliovirus, coxsackievirus B5, and echovirus 7 from 100-liter samples of seeded tap water were 54%, 27%, and 32%, respectively. There was no significant difference in virus recovery from tap water with a pH range of 6 to 9.5 and a water flow rate range of 5.5 liters/min to 20 liters/min. Finally, poliovirus and Norwalk virus recoveries by NanoCeram filters were compared to those by 1MDS filters, using tap water and Ohio River water. Poliovirus and Norwalk virus recoveries by NanoCeram filters from tap and river water were similar to or higher than those by the 1MDS filters. These data suggest that NanoCeram filters can be used as an inexpensive alternative to 1MDS filters for routine viral monitoring of water.

A method to remove environmental inhibitors prior to the detection of waterborne enteric viruses by reverse transcription-polymerase chain reaction

A method was developed to remove environmental inhibitors from sample concentrates prior to detection of human enteric viruses using the reverse transcription-polymerase chain reaction (RT-PCR). Environmental inhibitors, concentrated along with viruses during water sample processing, are removed by the method through a series of steps that includes dialysis, solvent extraction, ultrafiltration and glass purification. The method was tested by spiking sodium phosphate with poliovirus type 1 with or without humic or fulvic acids and then measuring virus recovery by plaque assay and RT-PCR. Results of the study indicated that (i) 90% of the spiked virus could be recovered from samples at the end of the ultrafiltration step, (ii) virus was detected in the final eluate of samples containing as much as 0.5 mg of humic acid or 5.0 mg of fulvic acid, and (iii) as little as 0.06 plaque forming units (PFU) was detectable per RT-PCR reaction. These results indicate that the described purification method along with RT-PCR is a feasible approach for detecting waterborne human enteric viruses in the presence of interfering substances.

Transport of viral specimens

The diagnosis of viral infections by culture relies on the collection of proper specimens, proper care to protect the virus in the specimens from environmental damage, and use of an adequate transport system to maintain virus activity. Collection of specimens with swabs that are toxic to either virus or cell culture should be avoided. A variety of transport media have been formulated, beginning with early bacteriological transport media. Certain swab-tube combinations have proven to be both effective and convenient. Of the liquid transport media, sucrose-based and broth-based media appear to be the most widely accepted and used. Studies on virus stability show that most viruses tested are sufficiently stable in transport media to withstand a transport time of 1 to 3 days. Some viruses may withstand longer transport times. In many cases, it is not necessary to store virus specimens in a refrigerator or send them to the laboratory on wet ice or frozen on dry ice. However, the specimen should not be exposed to environmental extremes. Modern viral transport media allow for more effective use of viral culture and culture enhancement techniques for the diagnosis of human viral infections.

Detecting Viruses in Water

Various and divergent approaches that have been used to concentrate and assay viruses from tap water and environmental freshwaters are summarized and briefly explained. The basic principles behind the different methodologies and descriptions of the most recent developments are emphasized. Comparisons help demonstrate the relative sensitivities of different concentration and assay techniques.

Efficient medium for impingement and storage of enveloped viruses

Airborne infections with pathogenic viruses play an important role in the transmission of diseases amongst men and animals. We compared several media intended for impingement of viruses from virus-contaminated air and for their preserving effect for two enveloped viruses. Sindbis (SINV) and vesicular stomatitis virus (VSV), members of the families Toga- and Rhabdoviridae, respectively, were chosen as indicator agents. Amongst the media tested, a sampling fluid consisting of phosphate buffered saline, pH 7.2, 0.5% bovine serum albumin, 0.5% gelatine (PBSplus) was most efficient to minimize the sampling stress during impingement and to preserve the infectivity SINV and VSV under stringent conditions at 37 degrees C. About 50% of virus infectivity was recovered 15.7 or 30 hours, respectively, after the beginning of storage. Thus the recommended medium is also suitable for shipment and storage of diagnostic virus samples.

Use of bituminous coal as an alternative technique for field concentration of waterborne viruses

A filter system that sandwiches a bituminous coal preparation between two prefilters was comparable to those presently used to recover human viruses from large volumes of water. This filter was effective over a pH range of 3.0 to 7.0. Poliovirus type 1 recoveries from 100-liter seeded samples of Cincinnati tap water did not vary significantly when compared with those of identical samples processed through Filterite and Millipore filters. In studies with raw domestic sewage, virus recoveries were nearly identical from comparable samples filtered through coal and Millipore disk filters. Thus, the availability of coal makes this filter system an inexpensive analytical tool, especially in developing nations, for virus concentration.