An improved infectivity assay combining cell culture with real-time PCR for rapid quantification of human adenoviruses 41 and semi-quantification of human adenovirus in sewage

UV inactivation of sewage isolated human adenovirus

Adenoviruses are known to be one of the most resistant viruses to UV disinfection. This study determined the inactivation kinetics of adenovirus freshly isolated from sewage samples, and compared the results with reference adenovirus stocks grown in the laboratory. Human adenoviruses were isolated from sewage samples using the HEK 293 cell line. Inactivation kinetics for UV irradiation was determined for monochromatic low pressure (LP) mercury UV lamp (254 nm) and polychromatic medium pressure (MP) mercury UV lamp for each sewage isolate. Eleven (11) isolates were obtained from nine (9) different sewage samples with most isolates belonging to the enteric adenovirus group, specifically adenovirus 41. The average dose required for 4 log inactivation using LP UV lamps for sewage isolates (220 mJ/cm²) was not significantly different (p > 0.1) from the average dose reported for lab-grown enteric adenovirus (179.6 mJ/cm²). Interestingly, the average dose required for 4 log inactivation using MP UV lamps was significantly higher (p = 0.004) for sewage isolates (124 mJ/cm²) when compared to the average dose reported for laboratory stocks of adenovirus 40 and 41 (71 mJ/cm²). Viral capsid analysis using the propidium monoazide (PMA)-qPCR method showed that adenovirus isolates from group F were less affected by exposure to MP UV Lamps than adenoviruses from group D and C. Adenovirus isolates obtained from sewage samples showed greater resistance to UV irradiation compared to laboratory grown strains, although required doses for MP UV were still considerably lower than LP UV. These data suggest that the required fluence for inactivation of adenoviruses in real-world waters may be higher than previously understood.

Rapid Assessment of SARS-CoV-2 Transmission Risk for Fecally Contaminated River Water

Following the outbreak of severe acute respiratory syndrome coronavirus (SARS-CoV-2), airborne water droplets have been identified as the main transmission route. Identifying and breaking all viable transmission routes are critical to stop future outbreaks, and the potential of transmission by water has been highlighted. By modifying established approaches, we provide a method for the rapid assessment of the risk of transmission posed by fecally contaminated river water and give example results for 39 countries. The country relative risk of transmission posed by fecally contaminated river water is related to the environment and the populations' infection rate and water usage. On the basis of in vitro data and using temperature as the primary controller of survival, we then demonstrate how viral loads likely decrease after a spill. These methods using readily available data suggest that sewage spills into rivers within countries with high infection rates could provide infectious doses of >40 copies per 100 mL of water. The approach, implemented in the supplementary spreadsheet, can provide a fast estimate of the upper and lower viral load ranges following a riverine spill. The results enable evidence-based research recommendations for wastewater epidemiology and could be used to evaluate the significance of fecal-oral transmission within freshwater systems.

Rapid Assessment of SARS-CoV-2 Transmission Risk for Fecally Contaminated River Water

Following the outbreak of severe acute respiratory syndrome coronavirus (SARS-CoV-2), airborne water droplets have been identified as the main transmission route. Identifying and breaking all viable transmission routes are critical to stop future outbreaks, and the potential of transmission by water has been highlighted. By modifying established approaches, we provide a method for the rapid assessment of the risk of transmission posed by fecally contaminated river water and give example results for 39 countries. The country relative risk of transmission posed by fecally contaminated river water is related to the environment and the populations' infection rate and water usage. On the basis of in vitro data and using temperature as the primary controller of survival, we then demonstrate how viral loads likely decrease after a spill. These methods using readily available data suggest that sewage spills into rivers within countries with high infection rates could provide infectious doses of >40 copies per 100 mL of water. The approach, implemented in the supplementary spreadsheet, can provide a fast estimate of the upper and lower viral load ranges following a riverine spill. The results enable evidence-based research recommendations for wastewater epidemiology and could be used to evaluate the significance of fecal-oral transmission within freshwater systems.

Viral indicators for tracking domestic wastewater contamination in the aquatic environment

Waterborne enteric viruses are an emerging cause of disease outbreaks and represent a major threat to global public health. Enteric viruses may originate from human wastewater and can undergo rapid transport through aquatic environments with minimal decay. Surveillance and source apportionment of enteric viruses in environmental waters is therefore essential for accurate risk management. However, individual monitoring of the >100 enteric viral strains that have been identified as aquatic contaminants is unfeasible. Instead, viral indicators are often used for quantitative assessments of wastewater contamination, viral decay and transport in water. An ideal indicator for tracking wastewater contamination should be (i) easy to detect and quantify, (ii) source-specific, (iii) resistant to wastewater treatment processes, and (iv) persistent in the aquatic environment, with similar behaviour to viral pathogens. Here, we conducted a comprehensive review of 127 peer-reviewed publications, to critically evaluate the effectiveness of several viral indicators of wastewater pollution, including common enteric viruses (mastadenoviruses, polyomaviruses, and Aichi viruses), the pepper mild mottle virus (PMMoV), and gut-associated bacteriophages (Type II/III FRNA phages and phages infecting human Bacteroides species, including crAssphage). Our analysis suggests that overall, human mastadenoviruses have the greatest potential to indicate contamination by domestic wastewater due to their easy detection, culturability, and high prevalence in wastewater and in the polluted environment. Aichi virus, crAssphage and PMMoV are also widely detected in wastewater and in the environment, and may be used as molecular markers for human-derived contamination. We conclude that viral indicators are suitable for the long-term monitoring of viral contamination in freshwater and marine environments and that these should be implemented within monitoring programmes to provide a holistic assessment of microbiological water quality and wastewater-based epidemiology, improve current risk management strategies and protect global human health.

Assessing the Occurrence of Waterborne Viruses in Reuse Systems: Analytical Limits and Needs

Detection of waterborne enteric viruses is an essential tool in assessing the risk of waterborne transmission. Cell culture is considered a gold standard for detection of these viruses. However, it is important to recognize the uncertainty and limitations of enteric virus detection in cell culture. Cell culture cannot support replication of all virus types and strains, and numerous factors control the efficacy of specific virus detection assays, including chemical additives, cell culture passage number, and sequential passage of a sample in cell culture. These factors can result in a 2- to 100-fold underestimation of virus infectivity. Molecular methods reduce the time for detection of viruses and are useful for detection of those that do not produce cytopathogenic effects. The usefulness of polymerase chain reaction (PCR) to access virus infectivity has been demonstrated for only a limited number of enteric viruses and is limited by an understanding of the mechanism of virus inactivation. All of these issues are important to consider when assessing waterborne infectious viruses and expected goals on virus reductions needed for recycled water. The use of safety factors to account for this may be useful to ensure that the risks in drinking water and recycled water for potable reuse are minimized.

Characteristics of olfactory ensheathing cells and microarray analysis in Tupaia belangeri (Wagner, 1841)

Tree shrews are most closely related to the primates and so possess a number of advantages in experimental studies; they have been used as an animal model in bacterial and virus infection, cancer, endocrine system disease, and certain nervous system diseases. Their olfactory ensheathing cells (OECs) are able to release several cytokines to promote neuronal survival, regeneration and remyelination. The present study used western blot analysis to identify antibody specificity in protein extracts from whole tree shrew brains to identify the specificity of p75 nerve growth factor receptor (NGFR) derived from rabbits (75 kDa). OECs were cultured and isolated, then stained and identified using the antibodies for p75NGFR. To investigate the capacity of OECs to express cytokines and growth factors, microarray technology was used, and the analysis revealed that OECs were able to express 9,821 genes. Of these genes, 44 genes were from the neurotrophic factor family, which may indicate their potential in transplantation in vivo. The present study considered the function of OECs as revealed by other studies, and may contribute to future research.

Progress in the study of virus detection methods: The possibility of alternative methods to validate virus inactivation

Virus inactivation validation studies have been widely applied in the risk assessment of biogenic material-based medical products, such as biological products, animal tissue-derived biomaterials, and allogeneic biomaterials, to decrease the risk of virus transmission. Traditional virus detection methods in an inactivation validation study utilize cell culture as a tool to quantify the infectious virus by observing cytopathic effects (CPEs) after virus inactivation. However, this is susceptible to subjective factors because CPEs must be observed by experts under a microscope during virus titration. In addition, this method is costly and time- and labor-consuming. Molecular biological technologies such as quantitative polymerase chain reaction (qPCR) have been widely used for virus detection but cannot distinguish infectious and noninfectious viruses. Therefore, qPCR cannot be directly applied to virus inactivation validation studies. In this paper, methods to detect viruses and progress in the challenge of differentiating infectious and noninfectious viruses with the combination of pretreatment and qPCR techniques such as the integrated cell culture-qPCR (ICC-qPCR) method are reviewed. In addition, the advantages and disadvantages of each new method, as well as its prospect in virus inactivation validation studies, are discussed.

Quantification of human adenovirus and norovirus in river water in the north-east of France

Human adenoviruses (HAdVs) are a major cause of infection and have been proposed as viral indicators of water quality. Human noroviruses (NoV) are the main cause of viral acute gastroenteritis. Quantitative data on the environmental prevalence of both viruses are needed. The genomes of HAdVs enteric adenovirus type 41 (HAdV41) and noroviruses of genogroups I and II (NoV GGI and GGII) were quantified over a 6-month period in a river located in north-eastern France. The samples were collected downstream from the discharge of a wastewater treatment plant. The viruses were concentrated using a glass wool method and the viral genomes were quantified using digital droplet PCR (ddPCR). All river water samples (15/15) were positive for the genomes of HAdVs, HAdV41, NoV GGI and NoV GGII. Concentrations of HAdVs, HAdV41 and NoV GII genomes were similar and HAdV41 represented ~ 80% of HAdVs. Infectious HAdVs were quantified in these samples using an integrated cell culture-quantitative PCR method (ICC-qPCR); they were detected in 93% (14/15) and quantified in 53% (8/15) of the samples. Thus, infectious HAdVs represented 0.3 to 12.2% of total HAdV particles detected by ddPCR. Infectious HAdV41 particles were found in 73% (11/15) of the samples. This common presence of pathogenic enteric viruses underlines the impact of wastewater discharge on quality of surface waters and may constitute a threat for human health. The relative abundance of genome of HAdV41 underlines the need for studies focusing on the specific detection of its infectious forms along water cycle.

Tertiary treatment and dual disinfection to improve microbial quality of reclaimed water for potable and non-potable reuse: A case study of facilities in North Carolina

Treated wastewater is increasingly of interest for either nonpotable purposes, such as agriculture and industrial use, or as source water for drinking water supplies; however, this type of advanced treatment for water supply is not always possible for many low resource settings. As an alternative, multiple barriers of physical, chemical and biological treatment with lower cost and simpler operation and maintenance have been proposed as more globally applicable. One such water reclamation system for both non-potable and potable reuse, is that approved by the State of North Carolina "for Type 2" reclaimed water (NCT2RW). NC Type 2 potable reuse systems consist of a sequence of tertiary treatment to produce well oxidized reclaimed water that is then then further treated by two steps of disinfection, typically UV radiation and chlorination. In this case study, the log10 microbial reduction performance of NCT2RW producing water reclamation facilities is evaluated. Based on the results presented here, NCT2RW consistently achieved high (6 for bacteria, 4 for virus and 4 for protozoan parasite surrogates) log10 reductions using the NC proposed treatment methods. Additionally, lower but significant log10 reduction performance was also documented for protozoan parasites and human enteric viruses.

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.

Long non-coding RNA linc01433 promotes migration and invasion in non-small cell lung cancer

Background

For many years, lung cancer has been the most common and deadly cancer worldwide. Early diagnosis of non‐small cell lung cancer (NSCLC) in particular is very difficult because the symptoms are often ignored. The five‐year survival rate is very low despite great improvements to therapy. Thus, there is an urgent need to identify prognostic biomarkers and target molecules for the clinical diagnosis and individualized treatment of NSCLC.

Methods

We performed quantitative real‐time PCR to determine the expression levels of the long non‐coding RNA (lncRNA) linc01433 in NSCLC and normal matched lung tissue. Subsequently, we established cell lines with overexpression or knockdown of linc01433 to evaluate the effects on proliferation and metastasis in vitro. Epithelial‐to‐mesenchymal transition was examined using Western blot.

Results

Linc01433 was significantly overexpressed in NSCLC tissues compared to normal lung tissues. In addition, linc01433 levels were associated with smoking history. Linc01433 overexpression in lung cancer cells increased proliferation, migration, and invasion abilities, as well as epithelial‐to‐mesenchymal transition.

Conclusions

Linc01433 is a cancer‐related lncRNA that may have an oncogene‐like effect in NSCLC.

Selection of cellular genetic markers for the detection of infectious poliovirus

AIMS

Cellular responses of an established cell line from human intestinal epithelial cells (INT-407 cells) against poliovirus (PV) infections were investigated in order to find cellular genetic markers for infectious PV detection.

METHODS AND RESULTS

Gene expression profile of INT-407 cells was analysed by DNA microarray technique when cells were infected with poliovirus 1 (PV1) (sabin) at multiplicity of infection of 10^-3 and incubated for 12 h. Poliovirus infection significantly altered the gene expressions of two ion channels, KCNJ4 and SCN7A. The expression profile of KCNJ4 gene was further investigated by real-time RT-qPCR, and it was found that KCNJ4 gene was significantly regulated at 24 h postinfection of PV1.

CONCLUSIONS

KCNJ4 gene, coding a potassium channel protein, is proposed as a cellular genetic marker for infectious PV detection.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first study to show the availability of cellular responses to detect infectious PV. The selection of cellular genetic markers for infectious viruses using DNA microarray and RT-qPCR can be applicable for the other enteric viruses.

From Lab to Lake - Evaluation of Current Molecular Methods for the Detection of Infectious Enteric Viruses in Complex Water Matrices in an Urban Area

Quantitative PCR methods are commonly used to monitor enteric viruses in the aquatic environment because of their high sensitivity, short reaction times and relatively low operational cost. However, conclusions for public health drawn from results of such molecular techniques are limited due to their inability to determine viral infectivity. Ethidium monoazide (EMA) and propidium monoazide (PMA) are capable to penetrate the damaged or compromised capsid of the inactivated viruses and bind to the viral nucleic acids. We assessed whether dye treatment is a suitable approach to improve the ability of qPCR to distinguish between infectious and non-infectious human adenovirus, enterovirus and rotavirus A in surface water of an urban river and sewage before and after UV disinfection. Like the gold standard of cell culture assays, pretreatment EMA-/PMA-qPCR succeeded in removing false positive results which would lead to an overestimation of the viral load if only qPCR of the environmental samples was considered. A dye pretreatment could therefore provide a rapid and relatively inexpensive tool to improve the efficacy of molecular quantification methods in regards to viral infectivity.

Technical aspects of using human adenovirus as a viral water quality indicator

Despite dramatic improvements in water treatment technologies in developed countries, waterborne viruses are still associated with many of cases of illness each year. These illnesses include gastroenteritis, meningitis, encephalitis, and respiratory infections. Importantly, outbreaks of viral disease from waters deemed compliant from bacterial indicator testing still occur, which highlights the need to monitor the virological quality of water. Human adenoviruses are often used as a viral indicator of water quality (faecal contamination), as this pathogen has high UV-resistance and is prevalent in untreated domestic wastewater all year round, unlike enteroviruses and noroviruses that are often only detected in certain seasons. Standard methods for recovering and measuring adenovirus numbers in water are lacking, and there are many variations in published methods. Since viral numbers are likely under-estimated when optimal methods are not used, a comprehensive review of these methods is both timely and important. This review critically evaluates how estimates of adenovirus numbers in water are impacted by technical manipulations, such as during adenovirus concentration and detection (including culturing and polymerase-chain reaction). An understanding of the implications of these issues is fundamental to obtaining reliable estimation of adenovirus numbers in water. Reliable estimation of HAdV numbers is critical to enable improved monitoring of the efficacy of water treatment processes, accurate quantitative microbial risk assessment, and to ensure microbiological safety of water.

High Incidence of Mammalian Orthoreovirus Identified by Environmental Surveillance in Taiwan

Wild poliovirus (WPV) persists in diverse locales worldwide, spreading outward from endemic areas. In response to the international threat of WPV transmission and changes in the national vaccination policy, we established an environmental surveillance system to monitor the circulation of wild and vaccine-related poliovirus in Taiwan. From July 2012 to December 2013, we collected sewage specimens every month from 10 sewage treatment plants located throughout Taiwan. The specimens were concentrated by the two-phase separation method and then inoculated into L20B, RD, and A549 cells for virus isolation. Viral isolates were identified and serotyped by immunofluorescence assay or molecular analysis. A total of 300 sewage samples were collected, and the results showed 163 samples (54.3%) were positive for virus, and 268 isolates were identified. Among these, 75 samples (25%) were positive for enterovirus (EV), but no poliovirus was found. In addition, 92 isolates were identified as enteroviruses and the most common serotypes were coxsackievirus B4, coxsackievirus B3, and coxsackievirus B2. Interestingly, 102 (34%) and 82 (27.3%) specimens were positive for mammalian orthoreovirus (MRV) and adenovirus, respectively. This study confirmed that sewage surveillance can be a useful additional modality for monitoring the possible presence of wild-type or vaccine-derived poliovirus in wastewater, and can indicate the current types of viruses circulating in the population. Furthermore, since MRV was found in children with acute necrotizing encephalopathy and meningitis, the high incidence of MRV detected by environmental surveillance warrants further investigation.

Quantitation of viable Coxiella burnetii in milk using an integrated cell culture-polymerase chain reaction (ICC-PCR) assay

The obligate intracellular pathogen Coxiella burnetii has long been considered the most heat resistant pathogen in raw milk, making it the reference pathogen for determining pasteurisation conditions for milk products. New milk formulations and novel non-thermal processes require validation of effectiveness which requires a more practical method for analysis than using the currently used animal model for assessing Coxiella survival. Also, there is an interest in better characterising thermal inactivation of Coxiella in various milk formulations. To avoid the use of the guinea pig model for evaluating Coxiella survival, an Integrated Cell Culture-PCR (ICC-PCR) method was developed for determining Coxiella viability in milk. Vero cell cultures were directly infected from Coxiella-contaminated milk in duplicate 24-well plates. Viability of the Coxiella in milk was shown by a ≥0·5 log genome equivalent (ge)/ml increase in the quantity of IS111a gene from the baseline post-infection (day 0) level after 9–11 d propagation. Coxiella in skim, 2%, and whole milk, and half and half successfully infected Vero cells and increased in number by at least 2 logs using a 48-h infection period followed by 9-d propagation time. As few as 125 Coxiella ge/ml in whole milk was shown to infect and propagate at least 2 logs in the optimised ICC-PCR assay, though variable confirmation of propagation was shown for as low as 25 Coxiella ge/ml. Applicability of the ICC-PCR method was further proven in an MPN format to quantitate the number of viable Coxiella remaining in whole milk after 60 °C thermal treatment at 0, 20, 40, 60 and 90 min.

Applicability of integrated cell culture quantitative PCR (ICC-qPCR) for the detection of infectious adenovirus type 2 in UV disinfection studies

Practical difficulties of the traditional adenovirus infectivity assay such as intensive labor requirements and longer turnaround period limit the direct use of adenovirus as a testing microorganism for systematic, comprehensive disinfection studies. In this study, we attempted to validate the applicability of integrated cell culture quantitative PCR (ICC-qPCR) as an alternative to the traditional cell culture method with human adenovirus type 2 (HAdV2) in a low-pressure UV disinfection study and to further optimize the procedures of ICC-qPCR for 24-well plate format. The relatively high stability of the hexon gene of HAdV2 was observed after exposure to UV radiation, resulting in a maximum gene copy reduction of 0.5 log10 at 280 mJ cm(-2). Two-day post-inoculation incubation period and a maximum spiking level of 10(5) MPN mL(-1) were selected as optimum conditions of ICC-qPCR with the tested HAdV2. An approximate 1:1 correlation of virus quantities by the traditional and ICC-qPCR cell culture based methods suggested that ICC-qPCR is a satisfactory alternative for practical application in HAdV2 disinfection studies. ICC-qPCR results, coupled with a first-order kinetic model (i.e., the inactivation rate constant of 0.0232 cm(2) mJ(-1)), showed that an UV dose of 172 mJ cm(-2) achieved a 4-log inactivation credit for HAdV2. This estimate is comparable to other studies with HAdV2 and other adenovirus respiratory types. The newly optimized ICC-qPCR shows much promise for further study on its applicability of other slow replicating viruses in disinfection studies.

Detection of pathogenic viruses in sewage provided early warnings of hepatitis A virus and norovirus outbreaks

Most persons infected with enterically transmitted viruses shed large amounts of virus in feces for days or weeks, both before and after onset of symptoms. Therefore, viruses causing gastroenteritis may be detected in wastewater, even if only a few persons are infected. In this study, the presence of eight pathogenic viruses (norovirus, astrovirus, rotavirus, adenovirus, Aichi virus, parechovirus, hepatitis A virus [HAV], and hepatitis E virus) was investigated in sewage to explore whether their identification could be used as an early warning of outbreaks. Samples of the untreated sewage were collected in proportion to flow at Ryaverket, Gothenburg, Sweden. Daily samples collected during every second week between January and May 2013 were pooled and analyzed for detection of viruses by concentration through adsorption to milk proteins and PCR. The largest amount of noroviruses was detected in sewage 2 to 3 weeks before most patients were diagnosed with this infection in Gothenburg. The other viruses were detected at lower levels. HAV was detected between weeks 5 and 13, and partial sequencing of the structural VP1protein identified three different strains. Two strains were involved in an ongoing outbreak in Scandinavia and were also identified in samples from patients with acute hepatitis A in Gothenburg during spring of 2013. The third strain was unique and was not detected in any patient sample. The method used may thus be a tool to detect incipient outbreaks of these viruses and provide early warning before the causative pathogens have been recognized in health care.