Rapid detection of human viruses in faeces by a simple and routine immune electron microscopy technique

Novel crAssphage marker genes ascertain sewage pollution in a recreational lake receiving urban stormwater runoff

Considerable efforts have been made in recent years in developing novel marker genes for fecal pollution tracking in environmental waters. CrAssphage are recently discovered DNA bacteriophage that are highly abundant in human feces and untreated sewage. In this study, we evaluated the host-sensitivity and -specificity of the newly designed crAssphage qPCR assays (Stachler et al., 2017) CPQ_056 and CPQ_064 (i.e., marker genes) in fecal samples collected from various human and several animal host groups in Australia. We also investigated the utility of these marker genes to detect sewage pollution in an urban recreational lake (i.e., Lake Parramatta) in Sydney, NSW. The mean concentrations of CPQ_056 and CPQ_064 marker genes in untreated sewage were 9.43 ± 0.14 log₁₀ GC/L and 8.91 ± 0.17 log₁₀ GC/L, respectively, 2 to 3 orders of magnitude higher than other sewage-associated viruses used in microbial source tracking studies. Among 177 animal fecal samples tested from 11 species, the host-specificity values for CPQ_056 and CPQ_064 marker genes were 0.95 and 0.93, respectively. Limited cross-reactivity was observed with cat fecal and cattle wastewater samples. Abundance of crAssphage markers were monitored in an urban lake that receives stormwater runoff. The concentrations of both markers were higher (CPQ_056 ranging from 3.40 to 6.04 log₁₀ GC/L and CPQ_064 ranging from 2.90 to 5.47 log₁₀ GC/L) in 20 of 20 (for CPQ_056) and 18 of 20 (for CPQ_064) samples collected after storm events with gauged sewer overflows compared to dry weather event (10 of 10 samples were qPCR negative for the CPQ_056 and 8 of 10 were negative for the CPQ_064 marker genes) suggesting sewage pollution was transported by urban stormwater runoff to Lake Parramatta. The results of the study may provide context for management of sewage pollution from gauged overflow points of the sewerage system in the catchment.

Astrovirus Diagnostics

Various methods exist to detect an astrovirus infection. Current methods include electron microscopy (EM), cell culture, immunoassays, polymerase chain reaction (PCR) and various other molecular approaches that can be applied in the context of diagnostic or in surveillance studies. With the advent of metagenomics, novel human astrovirus (HAstV) strains have been found in immunocompromised individuals in association with central nervous system (CNS) infections. This work reviews the past and current methods for astrovirus detection and their uses in both research laboratories and for medical diagnostic purposes.

Single-step antibody-based affinity cryo-electron microscopy for imaging and structural analysis of macromolecular assemblies

Single particle cryo-electron microscopy (cryo-EM) is an emerging powerful tool for structural studies of macromolecular assemblies (i.e., protein complexes and viruses). Although single particle cryo-EM requires less concentrated and smaller amounts of samples than X-ray crystallography, it remains challenging to study specimens that are low-abundance, low-yield, or short-lived. The recent development of affinity grid techniques can potentially further extend single particle cryo-EM to these challenging samples by combining sample purification and cryo-EM grid preparation into a single step. Here we report a new design of affinity cryo-EM approach, cryo-SPIEM, that applies a traditional pathogen diagnosis tool Solid Phase Immune Electron Microscopy (SPIEM) to the single particle cryo-EM method. This approach provides an alternative, largely simplified and easier to use affinity grid that directly works with most native macromolecular complexes with established antibodies, and enables cryo-EM studies of native samples directly from cell cultures. In the present work, we extensively tested the feasibility of cryo-SPIEM with multiple samples including those of high or low molecular weight, macromolecules with low or high symmetry, His-tagged or native particles, and high- or low-yield macromolecules. Results for all these samples (non-purified His-tagged bacteriophage T7, His-tagged Escherichiacoli ribosomes, native Sindbis virus, and purified but low-concentration native Tulane virus) demonstrated the capability of cryo-SPIEM approach in specifically trapping and concentrating target particles on TEM grids with minimal view constraints for cryo-EM imaging and determination of 3D structures.

Assessment of enteric viruses in a sewage treatment plant located in Porto Alegre, southern Brazil

In order to verify the microbial quality of the influents and effluents of one STP from southern Brazil, an eight-month survey was conducted to examine the presence of total and fecal coliforms and of adenovirus (HAdV), enterovirus (EV), genogroup A rotaviruses (GARV) and Torque teno virus (TTV), in treated effluent samples from São João/Navegantes STP, Porto Alegre (Brazil). A total of 16 samples were collected, eight of influent (raw sewage, prior to treatment), and the other eight of the effluent (post-treatment sewage). Total and fecal coliform levels ranging from 3.6 × 10(4) to 4.4 × 10(7) MPN/100 mL and 2.9 × 10(3) to 1.7 × 10(7) MPN/100 mL, were detected in all samples. In raw sewage, HAdV (25%) and GARV (28.6%) viral genomes were detected. The analysis of effluent samples revealed the presence of HAdV (50%), EV (37.5%), and TTV (12.5%) genomic fragments. All samples, regardless of the month analysed, presented detection of a least one virus genus, except for in April. Higher virus detection rates were observed in treated sewage samples (62.5%), and in 80% of them (effluent positive samples) HAdV was detected. Results showed that improvements in sewage monitoring and treatment processes are necessary to reduce the viral and bacterial load on the environment in southern Brazil. To the knowledge of the authors, this is the first study showing the monitoring of viral genomes in influent and effluent samples from a STP located in Porto Alegre (Rio Grande do Sul, Brazil), southern Brazil.

Risk of infectious gastroenteritis in young children living in Québec rural areas with intensive animal farming: results of a case-control study (2004-2007)

This study was designed to evaluate the epidemiology of severe gastroenteritis in children living in Québec rural areas with intensive livestock activities. From September 2005 through June 2007, 165 cases of gastroenteritis in children aged from 6 months to 5 years, hospitalized or notified to the public health department were enrolled, and 326 eligible controls participated. The parents of cases and controls were asked questions about different gastroenteritis risk factors. The quality of the drinking water used by the participants was investigated for microbial indicators as well as for four zoonotic bacterial pathogens (Campylobacter spp, Escherichia coli, Salmonella spp and Yersinia spp) and two enteric parasites (Cryptosporidium spp and Giardia spp). From 134 stool specimen analysed, viruses were detected in 82 cases (61%), while 28 (21%) were found with at least one of the bacteria investigated, and five cases were infected by parasites. Campylobacteriosis was the main bacterial infection (n = 15), followed by Salmonella sp (n = 7) and E. coli O157:H7 (n = 5) among cases with bacterial gastroenteritis. No significant difference was found between cases and controls regarding the quality of water consumed; the frequency of faecal contamination of private wells was also similar between cases and controls. Considering the total cases (including those with a virus), no link was found between severe gastroenteritis and either being in contact with animals or living in a municipality with the highest animal density (4th quartile). However, when considering only cases with a bacterial or parasite infection (n = 32), there was a weak association with pig density that was not statistically significant after adjusting for potential confounders. Contact with domestic, zoo or farm animals were the only environmental factor associated with the disease.

Rotavirus infection in a tertiary hospital: laboratory diagnosis and impact of immunization on pediatric hospitalization

BACKGROUND AND OBJECTIVES

Rotavirus (RV) is the main etiological agent of diarrhea in childhood; its laboratory diagnosis is crucial to guide the clinical management and prevention of its spread. RV immunization was introduced in Brazilian 6-month-old children in 2006. The present study was aimed to evaluate three methodologies used for human RV detection in stool samples obtained from patients hospitalized due to gastroenteritis in a teaching hospital and report the impact of RV immunization in hospitalization by diarrhea.

METHODS

293 stool samples collected in the 2001-2008 period were analyzed by enzyme immunoassay (EIA), latex agglutination (LA) and polyacrylamide gel electrophoresis (PAGE).

RESULTS

Rotavirus was detected in 34.8% of samples by LA assay, 28.3% of samples by EIA assay and in 25.6% of samples by PAGE assay. Considering the PAGE method as gold standard, the sensitivity, specificity and accuracy of EIA were 94.6%, 94.4% and 94.5%, and to LA were 82.6%, 81.6% and 81.9%, respectively.

CONCLUSION

These results indicate that antigen detection by EIA is a rapid, sensitive and specific method, and could be used in large-scale applications for screening stool samples suspected of RV infection. This study showed decreased incidence of RV infection in hospitalized children prior to the implementation of the national immunization program against RV.

Development of antigen-capture enzyme-linked immunosorbent assay and RT-PCR for detection of turkey astroviruses

Turkey astrovirus (TAstV) is an important agent of poult enteritis. The diagnosis of astroviruses has been dependent mainly on electron microscopy (EM) or immune EM (IEM). To develop other simple, rapid, and reliable diagnostic assays, two antigen-capture enzyme-linked immunosorbent assays (AC-ELISAs), polyclonal AC-ELISA and monoclonal AC-ELISA, were developed in this study. Monoplex and multiplex reverse transcription-polymerase chain reactions (RT-PCRs) were also developed using nondegenerate primer sets specific to the capsid region and degenerate primer pairs specific to the polymerase area of two TAstV. EM was included for comparison. Fecal or intestinal contents samples from naturally and experimentally infected poults with enteritis were examined using the developed assays. The polyclonal AC-ELISA had higher sensitivity and wider detection spectrum than the monoclonal AC-ELISA with group-specific monoclonal antibody (MAb), whereas the monoclonal AC-ELISA had very high specificity but lower sensitivity, which was estimated at 0.06 microg of viral proteins. Small round viruses (SRV) that could be astroviruses or other small viruses were detected in 34.4% of the samples examined by EM. The monoplex RT-PCR results amplified with primers SRV-1-3 and SRV-1-5 revealed that the positive rate of astroviruses was 45.3%, which was 10.9% higher than that of EM even if other SRVs were not excluded. Multiplex RT-PCR with SRV-1-3 and SRV-1-5 and AFCP-F1 and AFCP-R1 and the monoplex RT-PCR with degenerate primers verified that the positive rate of astroviruses was 59.4%, which was 25% higher than that of EM. Both RT-PCRs showed good specificity and wider detection spectrum compared with earlier published data.

Special techniques in diagnostic electron microscopy

The power of electron microscopy as a diagnostic tool can be amplified considerably by the application of ancillary preparative and analytic methods. Subcellular chemistry and structure can be examined by various forms of microprobe analysis and by special staining methods, including cytochemical, immunocytochemical, and negative staining. Qualitative ultrastructural examination can be augmented by morphometric analysis. Correlative microscopic survey methods can be used as a means of targeting ultrastructural investigations. This article provides an overview of the use of these special techniques in the diagnosis and classification of tumors and other selected pathologic processes.

Negative staining in the detection of viruses in clinical specimens

Viruses have unique morphology and are therefore good candidates for negative staining. Negative staining with phosphotungstic acid (PTA) or uranyl acetate has facilitated the detection of many viruses in clinical specimens. Enhancement procedures have included the use of centrifugation and agar diffusion for concentrating virus particles, the use of solid phase capture reagents to trap virus particles and the use of secondary antibodies and electron dense markers to help visualize them. Techniques currently in use and employing negative staining include direct EM, immune electron microscopy (IEM), solid phase immune electron microscopy (SPIEM), colloidal gold-labeled protein A (PAG), solid phase IEM employing a second decorator antibody (SPIEMDAT), and solid phase IEM using colloided gold-labeled secondary antibodies (SPEIMDAGT). IEM methods assist with the detection of small viruses or viruses present in low numbers while PAG offers increased sensitivity over direct EM and IEM. In our experience the serum-in-agar (SIA) method is the most sensitive of the PAG IEM techniques for detection of rotavirus particles in clinical specimens. SPIEMDAT enhances the detection of small viruses which are often missed by other techniques due to background staining in specimens. SPEIMDAGT employing colloidal gold-labeled secondary antibody has increased sensitivity and offers the advantage of detecting viral antigen when whole virus particles are not visible. IEM techniques have recently been used for typing viruses using either monospecific antisera or monoclonal antibodies and colloidal gold-labeled secondary antibody.

Ability of TESTPACK ROTAVIRUS enzyme immunoassay to diagnose rotavirus gastroenteritis

TESTPACK ROTAVIRUS, a simple 10-min enzyme immunoassay, was compared with electron microscopy and Pathfinder enzyme immunoassay on feces from 172 patients of various ages with gastroenteritis. The percent sensitivities and specificities before blocking with antiserum were as follows: TESTPACK, 100% sensitivity and 99% specificity; Pathfinder, 95% sensitivity and 98% specificity. After blocking, the sensitivity and specificity, respectively, were 100% and 100% for TESTPACK and 95% and 99% for Pathfinder. TESTPACK ROTAVIRUS was more sensitive, but not significantly, than Pathfinder (P greater than 0.1) and the direct electron microscopy technique (P greater than 0.1).

Viral respiratory tract infection and exacerbations of asthma in adult patients

The role of viral respiratory tract infections in acute exacerbations of asthma was studied prospectively in 31 patients with atopic asthma aged 15-56 years. Patients recorded symptom scores for asthma and peak expiratory flow rate daily for 11 months. In addition, they reported for detailed clinical, functional, and virological study every four weeks and as soon as possible after the onset of worsening asthma or symptoms suggesting a respiratory tract infection. Thirty viral identifications were made, of which 18 (60%) were associated with an exacerbation of asthma. Viral respiratory tract infection was identified in 18 (10%) of the 178 exacerbations of asthma, and in 10 (36%) of the 28 severe exacerbations. The frequency of viral identifications in 16 non-asthmatic, control subjects during the same period was similar. It is concluded that viral respiratory tract infections may cause or be associated with exacerbations of asthma in adults, and that they are an important factor in severe exacerbations.

Comparison of methods for concentration and purification of bovine viral diarrhea virus

The NADL strain of bovine viral diarrhea virus (BVDV) was concentrated by hollow fiber ultrafiltration or polyethylene glycol and purified by centrifugation through sucrose or potassium tartrate gradients. The protein content of polyethylene glycol concentrates was much lower than that of ultrafiltration concentrates. Conversely, recoveries of infectivity were greater using polyethylene glycol (100%) as compared to ultrafiltration (50%). Sucrose or potassium tartrate density gradients appeared comparable in purification of BVD virus. Peak infectivity fractions in both gradients corresponded quite well, having densities of 1.12-1.14 g/cm3, and showed a 150-fold reduction of protein when compared to crude viral supernate. Further examination by negative stain electron microscopy revealed integral pleomorphic, roughly spherical particles in both purified virus preparations. Small knob-like projections could be seen on viral particles.

Use of protein A in the serum-in-agar diffusion method in immune electron microscopy for detection of virus particles in cell culture

A modified technique using protein A in the serum-in-agar (SIA) method for immune electron microscopy (IEM) was presented. Grids coated with staphylococcal protein A were floated on samples mounted on agar containing 2% antiserum and incubated at 37 C, for 60 min. After washing and staining, the grids were observed in an electron microscope. The effects of protein A on virus detection were evaluated using poliovirus and bovine rotavirus infected cell culture fluids. The results showed that the technique using protein A (PA-SIA) had at least 10-fold higher sensitivity for virus detection than the original SIA. The optimal concentration of protein A was 1 to 10 micrograms/ml for coating the grids to trap virus particles. The PA-SIA method was also compared with immunosorbent electron microscopy (ISEM). The former showed higher or at least the same sensitivity and some advantages in detecting antigen-antibody reaction than the latter method. These results indicate that our PA-SIA method may be superior to other IEM techniques presented previously for the detection and identification of viruses.

Immunonegative stain techniques for electron microscopic detection of viruses in human faeces

Immune electron microscopy techniques have for some years been applied to detection of viruses in clinical specimens, especially faecal samples, as both sensitivity and specificity are improved by use of specific antibody. The following review describes in detail different preparation methods and illustrates some of the results that may be obtained.

Immunoperoxidase method with human immune serum globulin for broad-spectrum detection of cultivable human enteric viruses: application to enumeration of cultivable viruses in environmental samples

The detection and enumeration of most cultivable human enteric viruses from water is possible if samples are first inoculated onto a suitable cell line such as MA-104 or BGM. Virus growth is then detected by an indirect immunoperoxidase method with human immune serum globulin as the source of antibody to most enteric viruses. The number of positive cell cultures in the immunoperoxidase assay is used to calculate the virus titer (as a most probable number) in the sample assayed.

Examination of the Rotazyme II enzyme immunoassay for the diagnosis of rotavirus gastroenteritis

Rotazyme II, which is a shorter version of Rotazyme (less than 3 h), was compared with electron microscopy and Rotazyme for sensitivity and specificity on 229 human stool specimens. Compared with electron microscopy, the newer assay was found to be 99.4% sensitive and 97.3% specific for an overall agreement of 98.7%. After resolution of discordant results by blocking tests, the Rotazyme II enzyme immunoassay was shown to be more sensitive than electron microscopy and, therefore, 100% specific.

Elimination of viruses and indicator bacteria at each step of treatment during preparation of drinking water at seven water treatment plants

Seven drinking water treatment plants were sampled twice a month for 12 months to evaluate the removal of indicator bacteria and cytopathogenic enteric viruses. Samples were obtained at each level of treatment: raw water, postchlorination, postsedimentation, postfiltration, postozonation, and finished (tap) water. Raw water quality was usually poor, with total coliform counts exceeding 105 to 106 CFU/liter and the average virus count in raw water of 3.3 most probable number of cytopathogenic units (MPNCU)/liter; several samples contained more than 100 MPNCU/liter. All plants distributed finished water that was essentially free of indicator bacteria as judged by analysis of 1 liter for total coliforms, fecal coliforms, fecal streptococci, coagulase-positive staphylococci, and Pseudomonas aeruginosa. The total plate counts at 20 and 35 degrees C were also evaluated as a measure of the total microbial population and were usually very low. Viruses were detected in 7% (11 of 155) of the finished water samples (1,000 liters) at an average density of 0.0006 MPNCU/liter the highest virus density measured being 0.2 MPNCU/liter. The average cumulative virus reduction was 95.15% after sedimentation and 99.97% after filtration and did not significantly decrease after ozonation or final chlorination. The viruses isolated from treated waters were all enteroviruses: poliovirus types 1, 2, and 3, coxsackievirus types B3, B4, and B5, echovirus type 7, and untyped picornaviruses.

An enteric coronavirus of the rabbit: detection by immunoelectron microscopy and identification of structural polypeptides

The immunoelectron microscopy (IEM) technique has been used for the detection of a rabbit enteric coronavirus (RECV). Immune serum was prepared in guinea pigs; the viral antigen used for the immunization procedure was obtained from the caecum of a sick rabbit, concentrated by centrifugation and purified on Percoll gradient. In order to identify the viral particles used in the immunization procedure, the protein pattern of the particles was determined by electrophoresis and compared with the pattern of other known coronaviruses. Analysis of structural polypeptides of the purified viral particles revealed a pattern similar to that reported for other coronaviruses. These polypeptides cross reacted with two other coronavirus specific immune sera (IBV and TGE). IEM assay of fecal samples collected from healthy and sick rabbits showed the presence of immune aggregates in specimens from both sick and healthy rabbits. Those aggregates contained viral particles sharing morphological characteristics with other coronaviruses. Furthermore, IEM assay was shown to be more sensitive than a direct EM procedure to detect coronavirus particles in rabbit feces. This assay also allowed the detection of a larger number of chronic carriers.

A simplified microwell pseudoreplica for the detection of viruses by electron microscopy and immunoelectron microscopy

Simplified procedures for immunoelectron microscopy (IEM) and electron microscopy (EM) are described. The procedures employ the principle of agar filtration and pseudoreplication. The modification consisted of the use of microwells for storage of gels with or without antiserum (for IEM or EM, respectively) and an array of containers in which pseudoreplication and negative staining were performed. The containers were prepared from 5 ml syringes from which the needle holding parts were cut. This device enabled simultaneous and rapid handling of specimens. With Sindbis virus as a model, our microwell pseudoreplica IEM (MW-PR-IEM) was compared to six other IEM techniques and was found to be the most rapid and sensitive technique. With the MW-PR-IEM technique, the specific minimal detection limit (detection of clumps) was 1.5 x 10(7) virus particles per ml, and the non-specific detection limit (detection of single virions) was 1.8 x 10(6) virus particles per ml.

Immunosorbent electron microscopy for detection of viruses

This chapter discusses the newer modifications of immunosorbent electron microscopy (ISEM) methods in both plant and animal virology. ISEM methods presented in the chapter include all the techniques where the “solid phase principle” is essential in a way similar to other solid phase immunoassays. These methods include (1) the antibody-coated grid technique (AB-CGT); (2) the protein A-coated grid technique (PA-CGT); (3) the protein A-coated bacteria technique (PA-CBT); and (4) the antigen-coated grid technique (AG-CGT). In all ISEM methods, one of the components of the system is adsorbed to a solid phase. In AG-CGT, PA-CGT, and AB-CGT, one of the reagents is adsorbed to an electron microscopic grid, while in PA-CBT protein A is naturally present on the surface of a bacterium that serves as a solid support. In ISEM methods, the viruses can be statistically evaluated and numerically expressed as number of virions per unit of area, and can, therefore, be statistically evaluated. Thus, these methods optimize the results of a test by quantifying the effects of the quality of the supporting grid, the time of adsorption, the pH, the presence of salts, and the type of staining. The ISEM also permits a detailed study of antigenic variations in the same genus of virus, and thus would visually pinpoint the type or strain differences.

Rapid viral diagnosis

There has been much interest and activity in the development of techniques for rapid viral diagnosis which would allow successful intervention in the treatment of patients or their contacts or in the control of viral diseases in the community. The greatest emphasis has been on techniques that permit viral detection directly in the clinical specimen, since these avoid the need to cultivate the agent, are feasible for detection of viruses that cannot be cultivated, and can detect virus in specimens in which the agent is no longer infectious. Direct methods used for viral detection include electron microscopy and various immunoassays which are based on demonstrating reactivity of viral antigen in the specimen with known viral antisera. The use of immunoassays for more rapid identification of viruses isolated in laboratory host systems and for selective detection of viral antigen in inoculated cell cultures even before the agents produce an observable effect has been an important advance in viral diagnosis by the approach of isolation and identification. The reliability of all specific viral identification procedures depends on the use of high quality viral antisera. Some of the problems previously encountered in preparing satisfactory viral immune reagents are being overcome through the availability of highly specific monoclonal antibodies produced by cell hybridization techniques. Virus-specific IgM antibody assays for rapid diagnosis have been improved greatly through the use of a "capture" technique in which antibody to the human mu chain is used in the solid phase to separate IgM from other serum components which might compete with IgM antibody or give nonspecific reactivity, and also through the availability of highly specific monoclonal antibodies to the human mu chain. A variety of simple assays for determination of viral antibody status have been developed, and many are commercially available. The reliability of some of these antibody assays has been improved through the incorporation of more suitable controls and through better definition of interpretations which should be made from test results.

A rotavirus staphylococcal co-agglutination test

A simple and rapid staphylococcal co-agglutination (SA) test for detection of rotavirus in human faecal specimens is described. A suspension of protein A-containing staphylococci coated with a rabbit hyperimmune serum against the rotavirus strain of calf diarrhoeae virus was used as reagent. Before the SA test, the faecal specimens were absorbed with a suspension of uncoated staphylococci. 34 of 36 rotavirus immune electron microscopy (IEM) positive samples showed a positive SA test, whereas none of 41 IEM negative specimens agglutinated the staphylococcal reagent. The SA test was as sensitive as an enzyme-linked immunosorbent assay (Rotazyme) and in our hands more sensitive than a latex agglutination test (Rotalex).

Comparison of three electron microscopy techniques for the detection of human rotaviruses

Rotavirus detection by direct electron microscopy was compared with direct and indirect immune electron microscopy techniques. The latter two approaches permitted the enumeration of 25 and 103 times more rotaviruses respectively, than direct electron microscopy. Also, 70% and 90% of the virus particles were aggregated by direct and indirect immune electron microscopy techniques respectively, thus facilitating their detection.

Rapid identification of viruses by a simple indirect immune electron microscopy technique using ferritin-labelled antibodies

A simple indirect immune electron microscopy technique using ferritin-labelled antibodies and negative staining to rapidly visualize and identify human viruses is described. The increased electron density given by the ferritin molecules, which also served as a reliable marker, has greatly facilitated virus detection.