Capsid-Damaging Effects of UV Irradiation as Measured by Quantitative PCR Coupled with Ethidium Monoazide Treatment

Inactivation efficacy and mechanisms of wavelength-specific UV sources for various strains of Legionella pneumophila serogroup 1

Infections of Legionnaires' disease in the United States caused by Legionella have increased ninefold between the years 2000-2018. Legionella harbored in biofilms or inside amoeba within premise plumbing can be more resistant to disinfectants, thus causing treatment challenges. Ultraviolet-light emitting diodes (UV-LEDs) are an emerging water disinfection technology with several advantages over conventional UV lamps. In this study, we evaluated the effects of UV-LEDs (255, 265, and 285 nm), a low-pressure (LP) mercury UV lamp (254 nm), and a bandpass filtered medium-pressure (MP) mercury UV lamp (220 nm) on properties and inactivation of three strains of L. pneumophila serogroup 1. The UV-LEDs emitting at 255 and 265 nm showed greater inactivation performance against all the strains compared to the UV-LED at 285 nm and the LP UV lamp at 254 nm. Our results showed that strains of the same serogroup exhibited different UV sensitivities. Analyses of DNA and protein damage revealed that UV exposure using 254, 255, and 265 nm predominantly causes DNA damage, while protein damage is predominant at 220 nm. Both DNA and protein damage were observed at 285 nm, but the extent of DNA damage was relatively less significant compared to the other wavelengths. Electric energy consumption analysis showed that water treatment using UV-LEDs is currently unsatisfactory compared to conventional LP UV lamps due to the mediocre wall plug efficiency (WPE) of UV-LEDs. However, recent studies indicate that the WPE of UV-LEDs is continuously improving. Overall, our study highlights that UV-LEDs are a promising technology for inactivating waterborne pathogens and have the potential to replace existing UV mercury lamps for water disinfection applications.

Activity- and gene-based quantification of enteric viruses, F- specific RNA phage genogroups, pepper mild mottle virus, and Escherichia coli in surface water

Polymerase chain reaction (PCR) is widely applied for the monitoring of pathogenic viruses in water environments. To date, several pretreatments to selectively detect genes from infectious viruses via PCR have been developed. This study was aimed to characterize and validate methods for quantifying active viruses and indicators and to evaluate the proportion of their active fractions in surface water (n = 42). Active E. coli and F-specific RNA phage (FRNAPH) genogroups were quantified using culture assays. In addition to these microbes, norovirus genogroups I (GI) and II, Aichi virus 1, and pepper mild mottle virus (PMMoV) were quantified by (reverse transcription)-quantitative PCR (RT-qPCR) with and without cis-dichlorodiammineplatinum (CDDP) treatment to exclude genes in inactive viruses. CDDP-RT-qPCR showed concentrations and detection frequencies comparable to or higher than culture assays. Consequently, although CDDP-RT-qPCR can suggest the presence of an inactive virus, it can also overestimate the activity of the virus in the environment. Differences between culture and CDDP-RT-qPCR and between CDDP-RT-qPCR and RT-qPCR varied among the viruses. CDDP-RT-qPCR showed a concentration comparable to the culture assay (within 1 log10 difference) in 93 % of positive samples for GI-FRNAPH but in <63 % of positive samples for GII- and GIII-FRNAPHs. GII-NoV was detected from 5 and 30 out of 42 samples via CDDP-RT-qPCR and RT-qPCR, respectively, and was suggested as inactivated by 2.0 log10 or higher in most of the samples. By contrast, concentrations of PMMoV determined by these two assays were not notably different. It is suggested that the operational conditions of wastewater treatment plants around the sites, rather than environmental stresses, affected the microbial inactivation. To better understand the infectivity of viruses in the environment, it is important to investigate them using sensitive detection methods at various sites, including the source of contamination.

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.

Capsid integrity detection of pathogenic viruses in waters: Recent progress and potential future applications

Waterborne diseases caused by pathogenic human viruses are a major public health concern. To control the potential risk of viral infection through contaminated waters, a rapid, reliable tool to assess the infectivity of pathogenic viruses is required. Recently, an advanced approach (i.e., capsid integrity (RT-)qPCR) was developed to discriminate intact viruses (potentially infectious) from inactivated viruses. In this approach, samples were pretreated with capsid integrity reagents (e.g., monoazide dyes or metal compounds) before (RT -)qPCR. These reagents can only penetrate inactivated viruses with compromised capsids to bind to viral genomes and prevent their amplification, but they cannot enter viruses with intact capsids. Therefore, only viral genomes of intact viruses were amplified or detected by (RT-)qPCR after capsid integrity treatment. In this study, we reviewed recent progress in the development and application of capsid integrity (RT-)qPCR to assess the potential infectivity of viruses (including non-enveloped and enveloped viruses with different genome structures [RNA and DNA]) in water. The efficiency of capsid integrity (RT-)qPCR has been shown to depend on various factors, such as conditions of integrity reagent treatment, types of viruses, environmental matrices, and the capsid structure of viruses after disinfection treatments (e.g., UV, heat, and chlorine). For the application of capsid integrity (RT-)qPCR in real-world samples, the use of suitable virus concentration methods and process controls is important to control the efficiency of capsid integrity (RT-)qPCR. In addition, potential future applications of capsid integrity (RT-)qPCR for determining the mechanism of disinfection treatment on viral structure (e.g., capsid or genome) and a combination of capsid integrity treatment and next-generation sequencing (NGS) (capsid integrity NGS) for monitoring the community of intact pathogenic viruses in water are also discussed. This review provides essential information on the application of capsid integrity (RT-)qPCR as an efficient tool for monitoring the presence of pathogenic viruses with intact capsids in water.

Effect of Ultraviolet-C Light-Emitting Diode Treatment on Disinfection of Norovirus in Processing Water for Reuse of Brine Water

Processes in the food industry that use large amounts of water have been an important cause of waterborne disease outbreaks, as they expose individuals to risks for waterborne disease transmission. Developing technologies to ensure the hygiene and safety of food-processing steps is an urgent concern from an economic perspective. Furthermore, economic benefits can be derived if the processed water can be reused under microbiologically safe conditions. Among the major manufacturing processes in the kimchi industry, the brining process for salted kimchi cabbages requires a considerable amount of brine (approximately 2,000–2,500 l/1,000 kg of raw cabbage). The aim of this study was to establish virucidal conditions with ultraviolet-C light-emitting diodes (UVC LEDs) that can ensure the microbiological safety of brine water samples with various turbidities for reuse after disinfection. For quantitative analysis, first of all, magnetic bead separation (MBS) technique was used to capture and recover the human norovirus (HuNoV) virus particles; propidium monoazide (PMA) combined with RT-qPCR (PMA-RT-qPCR) was subsequently used to selectively detect infectious norovirus. Overall, as the turbidity of the brine water samples increased, the reduction in the HuNoV genogroup II genotype 4 (HuNoV GII.4) levels by UVC LED disinfection decreased. The derived inactivation rate constant (k_inac) and inactivation curves (calculated using the log-linear model) were studied as a function of turbidity based on the exponential one-phase inactivation kinetics of HuNoV. Using an impeller system set at 100 rotations/min (rpm) with an eight-nephelometric turbidity unit (NTU) sample (the lowest turbidity studied), the k_inact based on the levels of viral genomic RNA concentrations was approximately 2.15-fold higher than that observed without rotation (0 rpm). Moreover, the k_inact increased 1.69-fold with a 56-NTU sample (the highest turbidity studied) when the impeller system was set at 100 rpm. UVC LED treatment decreased the HuNoV GII.4 population more effectively in conjunction with the impeller system (100 rpm) than without the impeller system. Our novel findings and model provide fundamental and scientific data that may help reuse brine water and ensure its microbiological safety through disinfection. Our study highlights the benefits of UVC LED treatment in successfully eliminating waterborne viruses in a prompt, resistance-reducing, and energy-efficient approach at the laboratory scale, which lays the foundation for future plant-scale studies of UVC LED-disinfection systems.

Capsid integrity RT-qPCR for the selective detection of intact SARS-CoV-2 in wastewater

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes have been detected in wastewater worldwide. However, the assessment of SARS-CoV-2 infectivity in wastewater has been limited due to the stringent requirements of biosafety level 3. The main objective of this study is to investigate the applicability of capsid integrity RT-qPCR for the selective detection of intact SARS-CoV-2 in wastewater. Three capsid integrity reagents, namely ethidium monoazide (EMA, 0.1-100 μM), propidium monoazide (PMA, 0.1-100 μM), and cis-dichlorodiammineplatinum (CDDP, 0.1-1000 μM), were tested for their effects on different forms (including free genomes, intact and heat-inactivated) of murine hepatitis virus (MHV), which was used as a surrogate for SARS-CoV-2. CDDP at a concentration of 100 μM was identified as the most efficient reagent for the selective detection of infectious MHV by RT-qPCR (CDDP-RT-qPCR). Next, two common virus concentration methods including ultrafiltration (UF) and polyethylene glycol (PEG) precipitation were investigated for their compatibility with capsid integrity RT-qPCR. The UF method was more suitable than the PEG method since it recovered intact MHV (mean ± SD, 38% ± 29%) in wastewater much better than the PEG method did (0.013% ± 0.015%). Finally, CDDP-RT-qPCR was compared with RT-qPCR alone for the detection of SARS-CoV-2 in 16 raw wastewater samples collected in the Greater Tokyo Area. Five samples were positive for SARS-CoV-2 when evaluated by RT-qPCR alone. However, intact SARS-CoV-2 was detected in only three positive samples when determined by CDDP-RT-qPCR. Although CDDP-RT-qPCR was unable to determine the infectivity of SARS-CoV-2 in wastewater, this method could improve the interpretation of positive results of SARS-CoV-2 obtained by RT-qPCR.

Kinetic Modeling of Slightly Acidic Electrolyzed Water Decay Characteristics in Fresh Cabbage Disinfection Against Human Norovirus

To consistently disinfect fresh vegetables efficiently, the decay of disinfectants such as chlorine, electrolyzed oxidizing water (EOW), ozonated water, and plasma-activated water during the disinfection maintenance stage needs to be understood. The aim of our study was to evaluate the changes in the inactivation kinetics of slightly acidic electrolyzed water (SAEW) against human norovirus (HuNoV), based on the cabbage-to-SAEW ratio. After disinfection of fresh cabbage with disinfected SAEW solution, SAEW samples were collected and analyzed for physicochemical properties such as pH, available chlorine concentrations (ACCs), and oxidation-reduction potential (ORP). SAEW virucidal effects were evaluated. We confirmed the decay of post-disinfection SAEW solution and demonstrated the different patterns of the decay kinetic model for HuNoV GI.6 and GII.4. In addition, the goodness of fit of the tested models based on a lower Akaike information criterion, root-mean-square error (RMSE), and residual sum of squares (RSS) was close to zero. In particular, the change in both the HuNoV GI.6 and GII.4 inactivation exhibited a strong correlation with the changes in the ACC of post-disinfection SAEW. These findings demonstrate that physicochemical parameters of SAEW play a key role in influencing the kinetic behavior of changes in the disinfection efficiency of SAEW during the disinfection process. Therefore, to optimize the efficiency of SAEW, it is necessary to optimize the produce-to-SAEW ratio in future studies.

Capsid integrity quantitative PCR to determine virus infectivity in environmental and food applications - A systematic review

Capsid integrity quantitative PCR (qPCR), a molecular detection method for infectious viruses combining azo dye pretreatment with qPCR, has been widely used in recent years; however, variations in pretreatment conditions for various virus types can limit the efficacy of specific protocols. By identifying and critically synthesizing forty-one recent peer-reviewed studies employing capsid integrity qPCR for viruses in the last decade (2009-2019) in the fields of food safety and environmental virology, we aimed to establish recommendations for the detection of infectious viruses. Intercalating dyes are effective measures of viability in PCR assays provided the viral capsid is damaged; viruses that have been inactivated by other causes, such as loss of attachment or genomic damage, are less well detected using this approach. Although optimizing specific protocols for each virus is recommended, we identify a framework for general assay conditions. These include concentrations of ethidium monoazide, propidium monoazide or its derivates between 10 and 200 μM; incubation on ice or at room temperature (20 - 25 °C) for 5-120 min; and dye activation using LED or high light (500-800 Watts) exposure for periods ranging from 5 to 20 min. These simple steps can benefit the investigation of infectious virus transmission in routine (water) monitoring settings and during viral outbreaks such as the current COVID-19 pandemic or endemic diseases like dengue fever.

Capsid integrity quantitative PCR to determine virus infectivity in environmental and food applications - A systematic review

Capsid integrity quantitative PCR (qPCR), a molecular detection method for infectious viruses combining azo dye pretreatment with qPCR, has been widely used in recent years; however, variations in pretreatment conditions for various virus types can limit the efficacy of specific protocols. By identifying and critically synthesizing forty-one recent peer-reviewed studies employing capsid integrity qPCR for viruses in the last decade (2009-2019) in the fields of food safety and environmental virology, we aimed to establish recommendations for the detection of infectious viruses. Intercalating dyes are effective measures of viability in PCR assays provided the viral capsid is damaged; viruses that have been inactivated by other causes, such as loss of attachment or genomic damage, are less well detected using this approach. Although optimizing specific protocols for each virus is recommended, we identify a framework for general assay conditions. These include concentrations of ethidium monoazide, propidium monoazide or its derivates between 10 and 200 μM; incubation on ice or at room temperature (20 - 25 °C) for 5-120 min; and dye activation using LED or high light (500-800 Watts) exposure for periods ranging from 5 to 20 min. These simple steps can benefit the investigation of infectious virus transmission in routine (water) monitoring settings and during viral outbreaks such as the current COVID-19 pandemic or endemic diseases like dengue fever.

Ozone disinfection kinetics of poliovirus 1 determined by cell culture assay, RT-qPCR and ethidium monoazide qPCR reduction in a continuous quench-flow reactor

AIMS

A continuous quench-flow (CQF) reactor was developed to collect samples at the reaction times of less than one second. The reactor is applied to determine ozone disinfection kinetics of poliovirus and to study whether EMA-qPCR can assess the viral infectivity after ozone disinfection.

METHODS

Ozone disinfection of poliovirus was conducted in the developed CQF, and the disinfection kinetics were tested in the range of 0·7-5·0 s at ozone concentration of 0·08 and 0·25 mg l^-1 . Inactivation, damage on viral genome and damage on capsid integrity were determined by plaque assay, quantitative reverse transcription polymerase chain reaction (RT-qPCR) and ethidium monoazide treatment coupled with RT-qPCR (EMA-qPCR), respectively.

RESULTS

By using CQF, 2·18 and 2·76 log₁₀ reductions were observed at the reaction time of 0·7 s and ozone concentration of 0·08 and 0·25 mg l^-1 , respectively, followed by tailing. Ozone disinfection kinetics of poliovirus 1 were better fit by the efficiency factor Hom model than by the Chick-Watson model, or the modified Chick-Watson model. Kinetics observed were similar between RT-qPCR and EMA-qPCR assays at the reaction times of <2·0 s and ozone concentrations of 0·08 and 0·25 mg l^-1 . At reaction times > 5 s, viral concentration evaluated by EMA-qPCR was reduced in comparison to stable RT-qPCR results. Both assays still underestimated the virus inactivation.

CONCLUSION

The simple developed reactor can be used to investigate viral ozone disinfection kinetics and to elucidate inactivation characteristics or mechanisms at very short exposure times.

SIGNIFICANCE AND IMPACT OF THE STUDY

The developed CQF reactor is beneficial for better understanding of virus inactivation by ozone, and the reactor can be used to better elucidate disinfection kinetics and mechanisms for future research. This work constitutes an important contribution to the existing knowledge of the application and limitation of the EMA/PMA-qPCR to assess virus infectivity after ozone disinfection.

Quantum Leap from Gold and Silver to Aluminum Nanoplasmonics for Enhanced Biomedical Applications

Nanotechnology has been used in many biosensing and medical applications, in the form of noble metal (gold and silver) nanoparticles and nanostructured substrates. However, the translational clinical and industrial applications still need improvements of the efficiency, selectivity, cost, toxicity, reproducibility, and morphological control at the nanoscale level. In this review, we highlight the recent progress that has been made in the replacement of expensive gold and silver metals with the less expensive aluminum. In addition to low cost, other advantages of the aluminum plasmonic nanostructures include a broad spectral range from deep UV to near IR, providing additional signal enhancement and treatment mechanisms. New synergistic treatments of bacterial infections, cancer, and coronaviruses are envisioned. Coupling with gain media and quantum optical effects improve the performance of the aluminum nanostructures beyond gold and silver.

Differences in Viral Disinfection Mechanisms as Revealed by Quantitative Transfection of Echovirus 11 Genomes

Virus inactivation mechanisms can be elucidated by methods that measure the loss of specific virus functionality (e.g., host attachment, genome internalization, and genome replication). Genome functionality is frequently assessed by PCR-based methods, which are indirect and potentially inaccurate; genome damage that affects detection by high-fidelity PCR enzymes may not adversely affect the ability of actual cellular enzymes to produce functional virus. Therefore, we developed here a transfection-based assay to quantitatively determine viral genome functionality by inserting viral RNA into host cells directly to measure their ability to produce new functional viruses from damaged viral genomes. Echovirus 11 was treated with ozone, free chlorine (FC), UV light at 254 nm (UV₂₅₄), or heat, and then the reductions in genome functionality and infectivity were compared. Ozone reduced genome functionality proportionally to infectivity, indicating that genome damage is the main mechanism of virus inactivation. In contrast, FC caused little or no loss of genome functionality compared to infectivity, indicating a larger role for protein damage. For UV₂₅₄, genome functionality loss accounted for approximately 60% of virus inactivation, with the remainder presumably due to protein damage. Heat treatment resulted in no reduction in genome functionality, in agreement with the understanding that heat inactivation results from capsid damage. Our results indicate that there is a fundamental difference between genome integrity reductions measured by PCR enzymes in previous studies and actual genome functionality (whether the genome can produce virus) after disinfection. Compared to PCR, quantitative transfection assays provide a more realistic picture of actual viral genome functionality and overall inactivation mechanisms during disinfection.IMPORTANCE This study provides a new tool for assessing virus inactivation mechanisms by directly measuring a viral genome's ability to produce new viruses after disinfection. In addition, we identify a potential pitfall of PCR for determining virus genome damage, which does not reflect whether a genome is truly functional. The results presented here using quantitative transfection corroborate previously suggested virus inactivation mechanisms for some virus inactivation methods (heat) while bringing additional insights for others (ozone, FC, and UV₂₅₄). The developed transfection method provides a more mechanistic approach for the assessment of actual virus inactivation by common water disinfectants.

Capsid Integrity qPCR—An Azo-Dye Based and Culture-Independent Approach to Estimate Adenovirus Infectivity after Disinfection and in the Aquatic Environment

Recreational, reclaimed and drinking source waters worldwide are under increasing anthropogenic pressure, and often contain waterborne enteric bacterial, protozoan, and viral pathogens originating from non-point source fecal contamination. Recently, the capsid integrity (ci)-qPCR, utilizing the azo-dyes propidium monoazide (PMA) or ethidium monoazide (EMA), has been shown to reduce false-positive signals under laboratory conditions as well as in food safety applications, thus improving the qPCR estimation of virions of public health significance. The compatibility of two widely used human adenovirus (HAdV) qPCR protocols was evaluated with the addition of a PMA/EMA pretreatment using a range of spiked and environmental samples. Stock suspensions of HAdV were inactivated using heat, UV, and chlorine before being quantified by cell culture, qPCR, and ci-qPCR. Apparent inactivation of virions was detected for heat and chlorine treated HAdV while there was no significant difference between ci-qPCR and qPCR protocols after disinfection by UV. In a follow-up comparative analysis under more complex matrix conditions, 51 surface and 24 wastewater samples pre/post UV treatment were assessed for enteric waterborne HAdV to evaluate the ability of ci-qPCR to reduce the number of false-positive results when compared to conventional qPCR and cell culture. Azo-dye pretreatment of non-UV inactivated samples was shown to improve the ability of molecular HAdV quantification by reducing signals from virions with an accessible genome, thereby increasing the relevance of qPCR results for public health purposes, particularly suited to resource-limited low and middle-income settings.

Viability RT-qPCR Combined with Sodium Deoxycholate Pre-treatment for Selective Quantification of Infectious Viruses in Drinking Water Samples

The presence of pathogenic viruses in drinking water is a major public health concern. Although viability RT-qPCR methods were developed to quantify infectious viruses, they may not always reflect viral infectivity, therefore leading to false-positive results. In this study, sodium deoxycholate (SD) pre-treatment was used to improve the efficiency of viability RT-qPCR methods with respect to exclusive quantification of infectious viruses. The ability of SD pre-treatment to enhance the penetration of three viability markers, namely, ethidium monoazide (EMA, 100 µM), propidium monoazide (PMA, 100 µM), and cis-dichlorodiammineplatinum (CDDP, 1000 µM), into heat-treated (90 °C for 1 min) Aichi virus at various concentrations (0.01-0.5%) was evaluated. The optimal SD concentration was found to be 0.1% for all markers. EMA/PMA/CDDP-RT-qPCR with 0.1% SD pre-treatment was significantly more effective than without SD pre-treatment in determining AiV inactivation after heat (50, 60, 70, 80, or 90 °C for 1 min) or chlorine treatment (1 mgCl₂/L for 1, 2, 5, or 10 min). Among the viability RT-qPCR methods tested, CDDP-RT-qPCR with SD pre-treatment (SD-CDDP-RT-qPCR) was the most effective in reflecting viral infectivity. Performance testing of SD-CDDP-RT-qPCR in concentrated drinking water samples did not reveal any significant effects of SD-CDDP treatment. Thus, SD-CDDP-RT-qPCR could be a useful tool for monitoring infectious virus presence in drinking water.

Improving efficiency of viability-qPCR for selective detection of infectious HAV in food and water samples

AIM

To improve the efficacy of intercalating dyes to distinguishing between infectious and inactivated hepatitis A virus (HAV) in food.

METHODS AND RESULTS

Different intercalating dyes were evaluated for the discrimination between infectious and thermally inactivated HAV suspensions combining with the RT-qPCR proposed in the ISO 15216. Among them, PMAxx was the best dye in removing the RT-qPCR signal from inactivated HAV. Applied to lettuce and spinach, PMAxx-Triton pretreatment resulted in complete removal of the RT-qPCR signal from inactivated HAV. Likewise, this study demonstrates that this pretreatment is suitable for the discrimination of inactivated HAV in shellfish without further sample dilution. In mussels and oysters, the developed viability RT-qPCR method reduced the signal of inactivated HAV between 1·7 and 2·2 logs at high inoculation level, and signal was completely removed at low inoculation level.

CONCLUSIONS

This study showed that the use of PMAxx is an important improvement to assess HAV infectivity by RT-qPCR. It was shown that PMAxx-Triton pretreatment is suitable for the analysis of infectious HAV in complex food samples such as vegetables and shellfish.

SIGNIFICANCE AND IMPACT OF THE STUDY

The PMAxx-Triton pretreatment can be easily incorporated to the ISO norm for infectious virus detection.

Cold argon-oxygen plasma species oxidize and disintegrate capsid protein of feline calicivirus

Possible mechanisms that lead to inactivation of feline calicivirus (FCV) by cold atmospheric-pressure plasma (CAP) generated in 99% argon-1% O₂ admixture were studied. We evaluated the impact of CAP exposure on the FCV viral capsid protein and RNA employing several cultural, molecular, proteomic and morphologic characteristics techniques. In the case of long exposure (2 min) to CAP, the reactive species of CAP strongly oxidized the major domains of the viral capsid protein (VP1) leading to disintegration of a majority of viral capsids. In the case of short exposure (15 s), some of the virus particles retained their capsid structure undamaged but failed to infect the host cells in vitro. In the latter virus particles, CAP exposure led to the oxidation of specific amino acids located in functional peptide residues in the P2 subdomain of the protrusion (P) domain, the dimeric interface region of VP1 dimers, and the movable hinge region linking the S and P domains. These regions of the capsid are known to play an essential role in the attachment and entry of the virus to the host cell. These observations suggest that the oxidative effect of CAP species inactivates the virus by hindering virus attachment and entry into the host cell. Furthermore, we found that the oxidative impact of plasma species led to oxidation and damage of viral RNA once it becomes unpacked due to capsid destruction. The latter effect most likely plays a secondary role in virus inactivation since the intact FCV genome is infectious even after damage to the capsid.

Adenovirus Replication Cycle Disruption from Exposure to Polychromatic Ultraviolet Irradiation

Polychromatic ultraviolet (UV) light with bandwidth of 20 nm and peak emission centered at 224, 254, or 280 nm (UV₂₂₄, UV₂₅₄, and UV₂₈₀, respectively) were used to inactivate human adenovirus type 2 (HAdV-2). Quantitative polymerase chain reaction (qPCR) and reverse transcriptase qPCR assays were used to elucidate the step in the HAdV-2 replication cycle that was disrupted after UV exposure. UV treatment at any of the wavelengths analyzed did not inhibit association of HAdV-2 to the host cells even after exposure to a fluence (UV dose) that would produce a virus inactivation efficiency, measured by plaque assay, greater than 99.99%. In contrast, UV irradiation at all three peak emissions disrupted early E1A gene transcription and viral DNA replication, but different mechanisms appeared to be dominating such disruptions. UV₂₂₄ seemed to have little effect on the integrity of the viral genome but produced a structural transformation of the viral capsid that may inhibit the delivery of viral genome into the host cell nucleus. On the other hand, UV₂₅₄ and UV₂₈₀ did not affect the integrity of the viral capsid, but the mutations they produced on the viral genome might cause the inhibition of the early gene transcription and DNA replication after the viral genome successfully translocated into the host cell nucleus.

Pretreatment with propidium monoazide/sodium lauroyl sarcosinate improves discrimination of infectious waterborne virus by RT-qPCR combined with magnetic separation

RT-qPCR allows sensitive detection of viral particles of both infectious and noninfectious viruses in water environments, but cannot discriminate non-infectious from infectious viruses. In this study, we aimed to optimize RT-qPCR-based detection of chlorine-inactivated human norovirus (NoV) and pepper mild mottle virus (PMMoV) in suspension by pretreatment with an optimal combination of a monoazide and a detergent that can efficiently penetrate damaged viral capsids. Four methods were compared to determine the efficacy of chlorine disinfection (at 1, 3, and 5 min mg/L): (A) RT-qPCR alone, (B) RT-qPCR assay preceded by magnetic bead separation for enrichment of viral particles (MBS-RT-qPCR), (C) MBS-RT-qPCR assay with pretreatment with propidium monoazide (PMA-MBS-RT-qPCR), and (D) PMA-MBS-RT-qPCR assay with pretreatment with sodium lauroyl sarcosinate (INCI-PMA-MBS-RT-qPCR). On the basis of a PMA optimization assay, 200 and 300 μM PMA were used in subsequent experiments for NoV GII.4 and PMMoV, respectively. Optimal INCI concentrations, having minimal influence on NoV GII.4 and PMMoV, were found to be 0.5% and 0.2% INCI, respectively. For NoV GII.4, there were significant differences (P < 0.05) in log₁₀ genome copies between the PMA-treated and the INCI + PMA-treated samples (log₁₀ genome copies differed by 1.11 and 0.59 log₁₀ for 3 and 5 min mg/L of chlorine, respectively). For PMMoV, INCI induced differences in log₁₀ genome copies of 0.92, 1.18, and 1.86, for 1, 3, and 5 min mg/L of chlorine, respectively. Overall, the results of this study indicate that an optimal combination of PMA and INCI could be very useful for evaluating disinfection methods in water treatment strategies.

Wavelength-Dependent Damage to Adenoviral Proteins Across the Germicidal UV Spectrum

Adenovirus, a waterborne pathogen responsible for causing bronchitis, pneumonia, and gastrointestinal infections, is highly resistant to UV disinfection and therefore drives the virus disinfection regulations set by the U.S. Environmental Protection Agency. Polychromatic UV irradiation has been shown to be more effective at inactivating adenovirus and other viruses than traditional monochromatic irradiation emitted at 254 nm; the enhanced efficacy has been attributed to UV-induced damage to viral proteins. This research shows UV-induced damage to adenoviral proteins across the germicidal UV spectrum at wavelength intervals between 200 and 300 nm. A deuterium lamp with bandpass filters and UV light-emitting diodes (UV LEDs) isolated wavelengths in approximate 10 nm intervals. Sodium dodecyl sulfate polyacrylamide gel electrophoresis and image densitometry were used to detect signatures for the hexon, penton, fiber, minor capsid, and core proteins. The greatest loss of protein signature, indicating damage to viral proteins, occurred below 240 nm. Hexon and penton proteins exposed to a dose of 28 mJ/cm² emitted at 214 nm were approximately 4 times as sensitive and fiber proteins approximately 3 times as sensitive as those exposed to a dose of 50 mJ/cm² emitted at 254 nm. At 220 nm, a dose of 38 mJ/cm² reduced the hexon and penton protein quantities to approximately 33% and 31% of the original amounts, respectively. In contrast, a much higher dose of 400 mJ/cm² emitted at 261 and 278 nm reduced the original protein quantity to between 66-89% and 80-93%, respectively. No significant damage was seen with a dose of 400 mJ/cm² at 254 nm. This research directly correlates enhanced inactivation at low wavelengths with adenoviral protein damage at those wavelengths, adding fundamental insight into the mechanisms of inactivation of polychromatic germicidal UV irradiation for improving UV water disinfection.

Enzymatic and viability RT-qPCR assays for evaluation of enterovirus, hepatitis A virus and norovirus inactivation: Implications for public health risk assessment

AIM

To assess the potential of a viability dye and an enzymatic reverse transcription quantitative PCR (RT-qPCR) pretreatment to discriminate between infectious and noninfectious enteric viruses.

METHODS AND RESULTS

Enterovirus (EntV), norovirus (NoV) GII.4 and hepatitis A virus (HAV) were inactivated at 95°C for 10 min, and four methods were used to compare the efficiency of inactivation: (i) cell culture plaque assay for HAV and EntV, (ii) RT-qPCR alone, (iii) RT-qPCR assay preceded by RNase treatment, and (iv) pretreatment with a viability dye (reagent D (RD)) followed by RT-qPCR. In addition, heat-inactivated NoV was treated with RD coupled with surfactants to increase the efficiency of the viability dye. No treatment was able to completely discriminate infectious from noninfectious viruses. RD-RT-qPCR reduced more efficiently the detection of noninfectious viruses with little to no removal observed with RNase. RD-RT-qPCR method was the closest to cell culture assay. The combination of surfactants and RD did not show relevant improvements on the removal of inactivated viruses signal compared with viability RT-qPCR, with the exception of Triton X-100.

CONCLUSION

The use of surfactant/RD-RT-qPCR, although not being able to completely remove the signal from noninfectious viral particles, yielded a better estimation of viral infectivity.

SIGNIFICANCE AND IMPACT OF THE STUDY

Surfactant/RD-RT-qPCR may be an advantageous tool for a better detection of infectious viruses with potential significant impact in the risk assessment of the presence of enteric viruses.

Long amplicon (LA)-qPCR for the discrimination of infectious and noninfectious phix174 bacteriophages after UV inactivation

Waterborne viruses are increasingly being considered in risk assessment schemes. In general, virus detection by culture methods is time consuming. In contrast, detection by quantitative polymerase chain reaction (qPCR) is more rapid and therefore, more suitable for monitoring. At present, qPCR lacks the essential ability for discriminating between infectious and non-infectious viruses, thus limiting its applicability for monitoring disinfection processes. In this study, a method was developed to quantify UV inactivation by long amplicon (LA)-qPCR. Bacteriophage phiX174 was used as a surrogate for human pathogenic viruses. A qPCR protocol was developed with new sets of primers, resulting in amplicon lengths of 108, 250, 456, 568, 955, 1063, 1544, and 1764 nucleotides. The log reduction of gene copies increased with increasing amplicon length. Additional treatment with the intercalating dye, PMA, had no effect, indicating that the bacteriophage capsids were not damaged by low pressure UV irradiation. A qPCR of nearly the complete genome (approx. 5000 nucleotides) showed similar results to the plaque assay. The log reduction in qPCR correlates with [specific amplicon length x UV dose]. The normalized DNA effect constant can be applied to calculate phiX174 inactivation based on qPCR detection.

Application of viability PCR to discriminate the infectivity of hepatitis A virus in food samples

Transmitted through the fecal-oral route, the hepatitis A virus (HAV) is acquired primarily through close personal contact and foodborne transmission. HAV detection in food is mainly carried out by quantitative RT-PCR (RT-qPCR). The discrimination of infectious and inactivated viruses remains a key obstacle when using RT-qPCR to quantify enteric viruses in food samples. Initially, viability dyes, propidium monoazide (PMA) and ethidium monoazide (EMA), were evaluated for the detection and quantification of infectious HAV in lettuce wash water. Results showed that PMA combined with 0.5% Triton X-100 (Triton) was the best pretreatment to assess HAV infectivity and completely eliminated the signal of thermally inactivated HAV in lettuce wash water. This procedure was further evaluated in artificially inoculated foods (at concentrations of ca. 6×10(4), 6×10(3) and 6×10(2)TCID50) including lettuce, parsley, spinach, cockles and coquina clams. The PMA-0.5% Triton pretreatment reduced the signal of thermally inactivated HAV between 0.5 and 2 logs, in lettuce and spinach concentrates. Moreover, this pretreatment reduced the signal of inactivated HAV by more than 1.5 logs, in parsley and ten-fold diluted shellfish samples inoculated at the lowest concentration. Overall, this pretreatment (50 μM PMA-0.5% Triton) significantly reduced the detection of thermally inactivated HAV, depending on the initial virus concentration and the food matrix.