Comparative study of techniques used to recover viruses from residual urban sludge

Isolation of herpes simplex virus nucleocapsid DNA

As an inanimate virus, herpes simplex virus type 1 (HSV-1) necessarily encodes all of its functions in its DNA. Isolation of pure viral DNA allows multiple downstream applications, including the creation of recombinant HSV strains, cloning of selected regions, and sequencing of viral DNA. The term nucleocapsid refers to the combination of the viral genome with the enclosing capsid; these viral genomes are necessarily linear and have been packaged for egress, even if they are not yet released from the cell. In contrast, viral DNA that is not associated with capsids may include episomal or concatenated forms and may have modifications such as histones that are added within cells. During this protocol, the viral capsid protects the HSV genome from reagents that strip away and destroy most cellular contaminants. This procedure describes the isolation of viral nucleocapsids and their subsequent dissolution to purify clean, linear HSV DNA.

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.

Preliminary Study to Assess the Performance of Mengovirus Elution from Sludge

In the virus detection protocol for sludge, the viral elution step from solids to solution is critical. In this study, mengoviruses were detected in artificially contaminated sludge with a qRT-PCR assay. The viral yields ranged between 19 and 66 % for 60 % sludge. This study demonstrates that mengovirus can be used as a sample process control for analysis of sewage sludge.

Comparative analysis of rodent tissue preservation methods and nucleic acid extraction techniques for virus screening purposes

The polymerase chain reaction (PCR) has become an essential method for the detection of viruses in tissue specimens. However, it is well known that the presence of PCR inhibitors in tissue samples may cause false-negative results. Hence the identification of PCR inhibitors and evaluation and optimization of nucleic acid extraction and preservation methods is of prime concern in virus discovery programs dealing with animal tissues. Accordingly, to monitor and remove inhibitors we have performed comparative analyses of two commonly used tissue storage methods and five RNA purification techniques using a variety of animal tissues, containing quantified levels of added MS2 bacteriophages as the indicator of inhibition. The results showed (i) no significant difference between the two methods of sample preservation, viz. direct storage at -80°C or 4°C in RNAlater, (ii) lung rodent tissues contained lower levels of inhibitor than liver, kidney and spleen, (iii) RNA extraction using the EZ1+PK RNA kit was the most effective procedure for removal of RT-PCR inhibitors.

Balancing hygienization and anaerobic digestion of raw sewage sludge

The anaerobic digestion of raw sewage sludge was evaluated in terms of process efficiency and sludge hygienization. Four different scenarios were analyzed, i.e. mesophilic anaerobic digestion, thermophilic anaerobic digestion and mesophilic anaerobic digestion followed by a 60 °C or by an 80 °C hygienization treatment. Digester performance (organic matter removal, process stability and biogas yield) and the hygienization efficiency (reduction of Escherichia coli, somatic coliphages and F-specific RNA phages) were the main examined factors. Moreover, a preliminary economical feasibility study of each option was carried out throughout an energy balance (heat and electricity). The obtained results showed that both thermophilic anaerobic digestion and mesophilic anaerobic digestion followed by a hygienization step were able to produce an effluent sludge that fulfills the American and the European legislation for land application. However, higher removal efficiencies of indicators were obtained when a hygienization post-treatment was present. Regarding the energy balance, it should be noted that all scenarios have a significant energy surplus. Particularly, positive heat balances will be obtained for the thermophilic anaerobic digestion and for the mesophilic anaerobic digestion followed by 60 °C hygienization post-treatment if an additional fresh-sludge/digested sludge heat exchanger is installed for energy recovery.

Comparing extraction buffers to identify optimal method to extract somatic coliphages from sewage sludges

Somatic coliphages are present in high numbers in sewage sludge. Since they are conservative indicators of viruses during wastewater treatment processes, they are being used to evaluate the effectiveness of sludge treatment processes. However, efficient methods to extract them from sludge are lacking. The objective was to compare different virus extraction procedures and develop a method to extract coliphages from sewage sludge. Twelve different extraction buffers and procedures varying in composition, pH, and sonication were compared in their ability to recover indigenous phages from sludges. The 3% buffered beef extract (BBE) (pH 9.0), the 10% BBE (pH 9.0), and the 10% BBE (pH 7.0) with sonication were short-listed and their recovery efficiency was determined using coliphage-spiked samples. The highest recovery was 16% for the extraction that involved 10% BBE at pH 9.0. There is a need to develop methods to extract somatic phages from sludges for monitoring sludge treatment processes.

Development of a feasible method to extract somatic coliphages from sludge, soil and treated biowaste

Extraction of viruses and bacteriophages from sludge, soil and treated biowaste requires homogenization, elution, clarification and detoxification-decontamination steps. Seeding these matrixes with bacteriophages does not reproduce what happens in nature. Therefore, naturally occurring matrixes, raw sludge, digested and dewatered sludge and compost, containing high numbers of somatic coliphages, and soils contaminated with wastewater or raw sludge were used in the extraction assays. Based on eluting the bacteriophages with beef extract, a feasible method in which the different steps had been optimized has been established. The method is feasible, repeatable, robust and applicable in routine laboratories. Digested and dewatered sludge has been probed to be useful as a reference material for validation studies and for "in lab" quality control. The established method includes homogenization by magnetic stirring, elution (which is performed at the same time that homogenization) with 10% beef extract at neutral pH, clarification by centrifuging at 4000 x g and decontamination by filtration through low protein binding 0.22 microm diameter pore size membrane filters.

Production of rotavirus-like particles in tomato (Lycopersicon esculentum L.) fruit by expression of capsid proteins VP2 and VP6 and immunological studies

A number of different antigens have been successfully expressed in transgenic plants, and some are currently being evaluated as orally delivered vaccines. Here we report the successful expression of rotavirus capsid proteins VP2 and VP6 in fruits of transgenic tomato plants. By western blot analysis, using specific antibodies, we determined that the VP2 and VP6 produced in plants have molecular weights similar to those found in native rotavirus. The plant-synthesized VP6 protein retained the capacity to form trimers. We were able to recover rotavirus virus-like particles from tomato fruit (i.e., tomatoes) by centrifugation on a sucrose cushion and to visualize them by electron microscopy. This result indicated that VP2/VP6 can self-assemble into virus-like particles (VLPs) in plant cells, even though only a small proportion of VP2/VP6 assembled into VLPs. To investigate immunogenicity, adult mice were immunized intraperitoneally (i.p.) three times with a protein extract from a transgenic tomatoes in adjuvant. We found that the transgenic tomato extract induced detectable levels of anti-rotavirus antibodies in serum; however, we did not determine the contribution of either the free rotavirus proteins or the VLPs to the induction of the antibody response. These results suggest the potential of plant-based rotavirus VLPs for the development of a vaccine against rotavirus infection.

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).

Laboratory evaluation of thermophilic-anaerobic digestion to produce Class A biosolids. 2. Inactivation of pathogens and indicator organisms in a continuous-flow reactor followed by batch treatment

Thermophilic-anaerobic digestion in a single-stage, mixed, continuous-flow reactor is not approved in the United States as a process capable of producing Class A biosolids for land application. This study was designed to evaluate the inactivation of pathogens and indicator organisms in such a reactor followed by batch treatment in a smaller reactor. The combined process was evaluated at 53 degrees C with sludges from three different sources and at 51 and 55 degrees C with sludge from one of the sources. Feed sludge to the continuous-flow reactor was spiked with the pathogen surrogates Ascaris suum and vaccine-strain poliovirus. Feed and effluent were analyzed for these organisms and for indigenous Salmonella spp., fecal coliforms, Clostridium perfringens spores, and somatic and male-specific coliphages. No viable Ascaris eggs were observed in the effluent from the continuous reactor at 53 or 55 degrees C, with greater than 2-log removals across the digester in all cases. Approximately 2-log removal was observed at 51 degrees C, but all samples of effluent biosolids contained at least one viable Ascaris egg at 51 degrees C. No viable poliovirus was found in the digester effluent at any of the operating conditions, and viable Salmonella spp. were measured in the digester effluent in only one sample throughout the study. The ability of the continuous reactor to remove fecal coliforms to below the Class A monitoring limit depended on the concentration in the feed sludge. There was no significant removal of Clostridium perfringens across the continuous reactor under any condition, and there also was limited removal of somatic coliphages. The removal of male-specific coliphages across the continuous reactor appeared to be related to temperature. Overall, at least one of the Class A pathogen criteria or the fecal coliform limit was exceeded in at least one sample in the continuous-reactor effluent at each temperature. Over the range of temperatures evaluated, the maximum time required to meet the Class A criteria by batch treatment of the continuous-reactor effluent was 1 hour for Ascaris suum and Salmonella spp. and 2 hours for fecal coliforms.