Reactivity of Viral Nucleic Acids with Chlorine and the Impact of Virus Encapsidation

Comparison of sample pretreatments used to distinguish between infectious and non-infectious foodborne viruses by RT-qPCR

To detect viruses such as hepatitis A virus (HAV) and human norovirus (HuNoV) in foods, RT-qPCR or other molecular methods are used, which cannot distinguish between infectious and non-infectious virions. Samples can be pretreated to limit detection to intact and presumably infectious virions. We compared propidium monoazide (PMA or PMAxx), platinum (IV) chloride (PtCl4), magnetic silica beads and centrifugal filter using HAV or HuNoV inactivated by heat, pulsed light, or sodium hypochlorite (NaOCl). PMAxx completely or nearly eliminated (3.96 ± 1.24 log gc) the RT-qPCR signal of HAV inactivated at 100°C for 10 min. Pretreatments could not reduce significantly RT-qPCR signal of HAV after pulsed light (0.74 ± 0.36 log gc) and NaOCl (0.24 ± 0.14 log gc) inactivation. Enzymatic treatments did not improve the results obtained with PMAxx. The exudate of raspberry, strawberry or oyster used as food matrices needed dilution by at least tenfold for PMAxx to to yield results comparable to virions without a food matrix. Overall, PMAxx shows good potential to discriminate between infectious and non-infectious despite some remaining limitations.

Persistence of crAssBcn phages in conditions of natural inactivation and disinfection process and their potential role as human source tracking markers

Due to their abundance in the human gut, human specificity, and global distribution, some crAss-like phages, including the original p-crAssphage, have been proposed as indicators of human fecal pollution suitable for microbial source tracking (MST). The prevalence of crAss-like phages in water, and consequently their usefulness as MST indicators, is determined by their ability to survive various inactivation and disinfection processes. Recently, we isolated new crAss-like phages (named crAssBcn phages) capable of infecting Bacteroides intestinalis and exhibiting a wide geographical distribution. Here, we assessed the infectivity and DNA integrity of three crAssBcn phages (ΦCrAssBcn6, 10, and 15) and ΦCrAss001, the first crAss-like phage isolated, at different pHs and temperatures, after UV and chlorine treatments, and under natural conditions. Their bacterial host, B. intestinalis and a siphovirus Bacteroides-infecting phage GA17-A were used as controls. Infectious crAssBcn phages remained stable for a month at 4, 22, and 37 °C, and at pH 7, but inactivated when exposed to pH 3. Infective crAssBcn phages decreased by 5 log10 after treatment with 10 ppm of chlorine for 1 min and after UV treatment at a fluence of 5.94 mJ/cm2. However, heat treatment at 60 and 70 °C resulted in only a moderate decrease (<1 log10 and almost 3 log10 units of reduction, respectively). Experiments under natural conditions in outdoor mesocosms revealed that inactivation rates for crAssBcn phages, as for the other microorganisms, were higher in summer (up to 6 log10) than in winter (<4 log10), suggesting a higher incidence of inactivation factors, such as sunlight and temperature, in the warmer months. B. intestinalis was significantly more prone to inactivation than phages in most conditions except for the irradiation treatment. In contrast, crAssBcn phage DNA remained stable, with minimal reduction under most of the tested conditions, except in the summer mesocosm and UV assays.

Persistence and free chlorine disinfection of human coronaviruses and their surrogates in water

The coronavirus disease 2019 pandemic illustrates the importance of understanding the behavior and control of human pathogenic viruses in the environment. Exposure via water (drinking, bathing, and recreation) is a known route of transmission of viruses to humans, but the literature is relatively void of studies on the persistence of many viruses, especially coronaviruses, in water and their susceptibility to chlorine disinfection. To fill that knowledge gap, we evaluated the persistence and free chlorine disinfection of human coronavirus OC43 (HCoV-OC43) and its surrogates, murine hepatitis virus (MHV) and porcine transmissible gastroenteritis virus (TGEV), in drinking water and laboratory buffer using cell culture methods. The decay rate constants of human coronavirus and its surrogates in water varied, depending on virus and water matrix. In drinking water without disinfectant addition, MHV showed the largest decay rate constant (estimate ± standard error, 2.25 ± 0.09 day-1) followed by HCoV-OC43 (0.99 ± 0.12 day-1) and TGEV (0.65 ± 0.06 day-1), while in phosphate buffer without disinfectant addition, HCoV-OC43 (0.51 ± 0.10 day-1) had a larger decay rate constant than MHV (0.28 ± 0.03 day-1) and TGEV (0.24 ± 0.02 day-1). Upon free chlorine disinfection, the inactivation rates of coronaviruses were independent of free chlorine concentration and were not affected by water matrix, though they still varied between viruses. TGEV showed the highest susceptibility to free chlorine disinfection with the inactivation rate constant of 113.50 ± 7.50 mg-1 min-1 L, followed by MHV (81.33 ± 4.90 mg-1 min-1 L) and HCoV-OC43 (59.42 ± 4.41 mg-1 min-1 L).

IMPORTANCE

This study addresses an important knowledge gap on enveloped virus persistence and disinfection in water. Results have immediate practical applications for shaping evidence-based water policies, particularly in the development of disinfection strategies for pathogenic virus control.

Influence of Amino Acid Substitutions in Capsid Proteins of Coxsackievirus B5 on Free Chlorine and Thermal Inactivation

The sensitivity of enteroviruses to disinfectants varies among genetically similar variants and coincides with amino acid changes in capsid proteins, although the effect of individual substitutions remains unknown. Here, we employed reverse genetics to investigate how amino acid substitutions in coxsackievirus B5 (CVB5) capsid proteins affect the virus' sensitivity to free chlorine and heat treatment. Of ten amino acid changes observed in CVB5 variants with free chlorine resistance, none significantly reduced the chlorine sensitivity, indicating a minor role of the capsid composition in chlorine sensitivity of CVB5. Conversely, a subset of these amino acid changes located at the C-terminal region of viral protein 1 led to reduced heat sensitivity. Cryo-electron microscopy revealed that these changes affect the assembly of intermediate viral states (altered and empty particles), suggesting that the mechanism for reduced heat sensitivity could be related to improved molecular packing of CVB5, resulting in greater stability or altered dynamics of virus uncoating during infection.

Mitigation of viruses of concern and bacteriophage surrogates via common unit processes for water reuse: A meta-analysis

Water reuse is a growing global reality. In regulating water reuse, viruses have come to the fore as key pathogens due to high shedding rates, low infectious doses, and resilience to traditional wastewater treatments. To demonstrate the high log reductions required by emerging water reuse regulations, cost and practicality necessitate surrogates for viruses for use as challenge organisms in unit process evaluation and monitoring. Bacteriophage surrogates that are mitigated to the same or lesser extent than viruses of concern are routinely used for individual unit process testing. However, the behavior of these surrogates over a multi-barrier treatment train typical of water reuse has not been well-established. Toward this aim, we performed a meta-analysis of log reductions of common bacteriophage surrogates for five treatment processes typical of water reuse treatment trains: advanced oxidation processes, chlorination, membrane filtration, ozonation, and ultraviolet (UV) disinfection. Robust linear regression was applied to identify a range of doses consistent with a given log reduction of bacteriophages and viruses of concern for each treatment process. The results were used to determine relative conservatism of surrogates. We found that no one bacteriophage was a representative or conservative surrogate for viruses of concern across all multi-barrier treatments (encompassing multiple mechanisms of virus mitigation). Rather, a suite of bacteriophage surrogates provides both a representative range of inactivation and information about the effectiveness of individual processes within a treatment train. Based on the abundance of available data and diversity of virus treatability using these five key water reuse treatment processes, bacteriophages MS2, phiX174, and Qbeta were recommended as a core suite of surrogates for virus challenge testing.

Virucidal efficacy of hypochlorous acid water for aqueous phase and atomization against SARS-CoV-2

Coronavirus disease 2019 (COVID-19) is an infectious viral disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that emerged at the end of 2019. SARS-CoV-2 can be transmitted through droplets, aerosols, and fomites. Disinfectants such as alcohol, quaternary ammonium salts, and chlorine-releasing agents, including hypochlorous acid, are used to prevent the spread of SARS-CoV-2 infection. In the present study, we investigated the efficacy of ionless hypochlorous acid water (HOCl) in suspension and by spraying to inactivate SARS-CoV-2. The virucidal efficacy of HOCl solution in tests against SARS-CoV-2 was evaluated as 50% tissue culture infectious dose. Although the presence of organic compounds influenced the virucidal efficacy, HOCl treatment for 20 s was significantly effective to inactivate Wuhan and Delta strains in the suspension test. HOCl atomization for several hours significantly reduced the SARS-CoV-2 attached to plastic plates. These results indicate that HOCl solution with elimination containing NaCl and other ions may have high virucidal efficacy against SARS-CoV-2. This study provides important information about the virucidal efficacy and use of HOCl solution.

Effectiveness of monochloramine for inactivation of coronavirus in reclaimed water

Fecal shedding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by infected persons into wastewater was documented early during the COVID-19 pandemic, thereby stimulating inquiries into the effectiveness of municipal wastewater treatment processes for the reduction of infectious viruses. In wastewater treatment plants, free chlorine has traditionally been the disinfectant utilized due to its low cost and high efficacy. However, regulations limiting disinfection by-products have prompted a shift to chloramination in many areas of the United States. While studies regarding the effectiveness of free chlorine against many viral agents are abundant, the efficacy of monochloramine (NH2Cl) has been less well researched. This study aimed to determine the effectiveness of pre-formed monochloramine for disinfection of human coronavirus 229E (HCoV-229E) in both phosphate-buffered saline (PBS) and reclaimed water from a water reclamation plant in Tucson, Arizona. Reclaimed water was sampled over the course of six months (August 2020 to November 2020), and dosed with monochloramine at 3 mg/L. An additional 1 mg/L free ammonia was added to simulate the operational conditions of the treatment plant. Viability was determined using MRC-5 host cell monolayers, using the TCID50 assay method. An average Ct99.9 (concentration of disinfectant multiplied by the contact time to achieve a 99.9 % reduction of the target organism) of 176 mg*min/L monochloramine was determined. No significant difference in inactivation rate was observed between the dosed reclaimed water and phosphate buffered saline (PBS). These data indicate that monochloramine is an effective disinfectant for coronaviruses. They also indicate that the water matrix type did not significantly impact the disinfection efficacy of monochloramine against HCoV-229E in reclaimed wastewater compared to PBS.

Inactivation Kinetics and Replication Cycle Inhibition of Coxsackievirus B5 by Free Chlorine

The kinetics of coxsackievirus serotype B5 (CVB5) inactivation with free chlorine is characterized over a range of pH and temperature relevant to drinking water treatment with the primary goal of selecting experimental conditions used for assessing inactivation mechanisms. The inactivation kinetics identified in our study is similar to or slower than experimental data reported in the literature and thus provides a conservative representation of the kinetics of CVB5 inactivation for free chlorine that could be useful in developing future regulations for waterborne viral pathogens including adequate disinfection treatment for CVB5. Untreated and free chlorine-treated viruses, and host cells synchronized-infected with these viruses, are analyzed by a reverse transcription-quantitative polymerase chain reaction (RT-qPCR) method with the goal of quantitatively investigating the effect of free chlorine exposure on viral genome integrity, attachment to host cell, and viral genome replication. The inactivation kinetics observed results from a combination of hindering virus attachment to the host cell, inhibition of one or more subsequent steps of the replication cycle, and possibly genome damage.

Bacteria and Virus Inactivation: Relative Efficacy and Mechanisms of Peroxyacids and Chlor(am)ine

Peroxyacids (POAs) are a promising alternative to chlorine for reducing the formation of disinfection byproducts. However, their capacity for microbial inactivation and mechanisms of action require further investigation. We evaluated the efficacy of three POAs (performic acid (PFA), peracetic acid (PAA), and perpropionic acid (PPA)) and chlor(am)ine for inactivation of four representative microorganisms (Escherichia coli (Gram-negative bacteria), Staphylococcus epidermidis (Gram-positive bacteria), MS2 bacteriophage (nonenveloped virus), and Φ6 (enveloped virus)) and for reaction rates with biomolecules (amino acids and nucleotides). Bacterial inactivation efficacy (in anaerobic membrane bioreactor (AnMBR) effluent) followed the order of PFA > chlorine > PAA ≈ PPA. Fluorescence microscopic analysis indicated that free chlorine induced surface damage and cell lysis rapidly, whereas POAs led to intracellular oxidative stress through penetrating the intact cell membrane. However, POAs (50 μM) were less effective than chlorine at inactivating viruses, achieving only ∼1-log PFU removal for MS2 and Φ6 after 30 min of reaction in phosphate buffer without genome damage. Results suggest that POAs' unique interaction with bacteria and ineffective viral inactivation could be attributed to their selectivity toward cysteine and methionine through oxygen-transfer reactions and limited reactivity for other biomolecules. These mechanistic insights could inform the application of POAs in water and wastewater treatment.

The Protective Effect of Virus Capsids on RNA and DNA Virus Genomes in Wastewater

Virus concentrations measured in municipal wastewater help inform both the water treatment necessary to protect human health and wastewater-based epidemiology. Wastewater measurements are typically PCR-based, and interpreting gene copy concentrations requires an understanding of the form and stability of the nucleic acids. Here, we study the persistence of model virus genomes in wastewater, the protective effects provided by the virus capsids, and the relative decay rates of the genome and infectious viruses. In benchtop batch experiments in wastewater influent at 25 °C, extraviral (+)ssRNA and dsDNA amplicons degraded by 90% within 15-19 min and 1.6-1.9 h, respectively. When encapsidated, the T90 for MS2 (+)ssRNA increased by 424× and the T90 for T4 dsDNA increased by 52×. The (+)ssRNA decay rates were similar for a range of amplicon sizes. For our model phages MS2 and T4, the nucleic acid signal in untreated wastewater disappeared shortly after the viruses lost infectivity. Combined, these results suggest that most viral genome copies measured in wastewater are encapsidated, that measured concentrations are independent of assay amplicon sizes, and that the virus genome decay rates of nonenveloped (i.e., naked) viruses are similar to inactivation rates. These findings are valuable for the interpretation of wastewater virus measurements.

Chlorinated nucleotides and analogs as potential disinfection byproducts in drinking water

Identification of emerging disinfection byproducts (DBPs) of health relevance is important to uncover the health risk of drinking water observed in epidemiology studies. In this study, mutagenic chlorinated nucleotides were proposed as potential DBPs in drinking water, and the formation and transformation pathways of these DBPs in chlorination of nucleotides were carefully investigated. A total of eleven chlorinated nucleotides and analogs were provisionally identified as potential DBPs, such as monochloro uridine/cytidine/adenosine acid and dichloro cytidine acid, and the formation mechanisms involved chlorination, decarbonization, hydrolysis, oxidation and decarboxylation. The active sites of nucleotides that reacted with chlorine were on the aromatic heterocyclic rings of nucleobases, and the carbon among the two nitrogen atoms in the nucleobases tended to be transformed into carboxyl group or be eliminated, further forming ring-opening or reorganization products. Approximately 0.2-4.0 % (mol/mol) of these chlorinated nucleotides and analogs finally decomposed to small-molecule aliphatic DBPs, primarily including haloacetic acids, trichloromethane, and trichloroacetaldehyde. Eight intermediates, particularly chlorinated imino-D-ribose and imino-D-ribose, were tentatively identified in chlorination of uridine. This study provides the first set of preliminary evidence for indicating the promising occurrence of chlorinated nucleotides and analogs as potential toxicological-relevant DBPs after disinfection of drinking water.

Inactivation of phage phiX174 by UV254 and free chlorine: Structure impairment and function loss

Disinfection is widely applied in water and wastewater treatment to inactivate viruses. However, the inactivation mechanism associated with viral structural alteration during disinfection is still not clear. In this work, inactivation of bacteriophage phiX174 by ultraviolet radiation (UV₂₅₄) and free chlorine (FC), two most commonly used disinfection processes, was studied at the molecular level to investigate the relationship between phiX174 genome impairment and virus inactivation, and the correlation between protein impairment and function loss. Double-layer agar technique, quantitative real-time polymerase chain reaction (qPCR), real-time reverse transcription-polymerase chain reaction (RT-qPCR), and liquid chromatography-tandem mass spectrometry techniques (LC-MS/MS), together with structure impairment and function experiments were implemented to quantitatively analyze the inactivation and damage to genome and proteins of phiX174. Results showed that UV₂₅₄ and FC could effectively inactivate phiX174 at the practical doses (UV₂₅₄ dose of 30 mJ/cm², and FC of 1-3 mg/L) used in water treatment plants, accompanied with the damage to viral genome and proteins. Specifically, a UV₂₅₄ irradiation dose of 9.6 mJ/cm², and FC at an initial concentration of 1 mg/L at 4 min could lead to a 4-log₁₀ inactivation. Nevertheless, the combination of these two methods at selected doses played no significant synergistic disinfection effect. During UV₂₅₄ disinfection, the proportion of phiX174 with damaged genome was similar with that of the inactivated phiX174. In addition, UV₂₅₄ and FC could disrupt proteins of phiX174 such as H protein, thereby hindering the physiological function associated with these proteins. With these findings, it is suggested that UV₂₅₄ and FC disinfection could hinder the injection of the viral genome into host cells, thus resulting in the inactivation of phiX174. This work provides a comprehensive study of the inactivation mechanism of phiX174, which can enhance the applicability of UV₂₅₄ and FC in water treatment plants, and facilitate the design and optimization of disinfection technologies for virus control in drinking water and wastewater worldwide to ensure the biosafety.

Persistence of endogenous RNA biomarkers of SARS-CoV-2 and PMMoV in raw wastewater: Impact of temperature and implications for wastewater-based epidemiology

Understanding the persistence of SARS-CoV-2 biomarkers in wastewater should guide wastewater-based epidemiology users in selecting best RNA biomarkers for reliable detection of the virus during current and future waves of the pandemic. In the present study, the persistence of endogenous SARS-CoV-2 were assessed during one month for six different RNA biomarkers and for the pepper mild mottle virus (PMMoV) at three different temperatures (4, 12 and 20 °C) in one wastewater sample. All SARS-CoV-2 RNA biomarkers were consistently detected during 6 days at 4° and differences in signal persistence among RNA biomarkers were mostly observed at 20 °C with N biomarkers being globally more persistent than RdRP, E and ORF1ab ones. SARS-CoV-2 signal persistence further decreased in a temperature dependent manner. At 12 and 20 °C, RNA biomarker losses of 1-log10 occurred on average after 6 and 4 days, and led to a complete signal loss after 13 and 6 days, respectively. Besides the effect of temperature, SARS-CoV-2 RNA signals were more persistent in the particulate phase compared to the aqueous one. Finally, PMMoV RNA signal was highly persistent in both phases and significantly differed from that of SARS-CoV-2 biomarkers. We further provide a detailed overview of the latest literature on SARS-CoV-2 and PMMoV decay rates in sewage matrices.

Inactivation and genome damage of rotavirus and a human norovirus surrogate by monochloramine treatment and sequential application with UV

The inactivation efficacy by monochloramine for disinfecting gastroenteritis-causing rotaviruses (RV) and Tulane viruses (TV), a surrogate for noroviruses, were evaluated in this study. In addition, the strategies for improving the disinfection efficiency of monochloramine by raising the temperature and sequentially implementing UV irradiation were investigated. The results showed that monochloramine was more effective in the inactivation of TV than RV. Additionally, the inactivation rate constants of RV and TV by monochloramine at 35 °C were improved approximately by 46% and 100%, respectively, compared to those at 25 °C. Moreover, applying UV irradiation before monochloramine enhanced the inactivation efficacy of RV and TV by 63% and 72% compared to monochloramine alone (UV: 6 mJ/cm², NH₂Cl: 60 ppm × min). Furthermore, the synergistic effect was observed during the RV inactivation by the sequential process. Especially, higher than 0.5 log₁₀ reductions of RV VP1 genome contributed to the synergistic effect in sequential treatment, while less than 0.1 log₁₀ reductions of RV VP1 genome were observed during UV alone (13 mJ/cm²) or monochloramine alone (94 ppm × min). The genome damage might be the primary mechanism of generating synergy in sequential treatment for the inactivation of RV. By comparison, no synergistic effect was discovered for the inactivation of TV due to high susceptibility to monochloramine and UV. The findings on the inactivation efficacy and mechanism for improvement will contribute to a wide application of monochloramine for virus inactivation in water treatment and distribution systems.

Chloride Enhances DNA Reactivity with Chlorine under Conditions Relevant to Water Treatment

Free available chlorine (FAC) is widely used to inactivate viruses by oxidizing viral components, including genomes. It is commonly assumed that hypochlorous acid (HOCl) is the chlorinating agent responsible for virus inactivation; however, recent studies have underscored that minor constituents of FAC existing in equilibrium with HOCl, such as molecular chlorine (Cl₂), can influence FAC reactivity toward select organic compounds. This study measures the FAC reaction kinetics with dsDNA and ssDNA extracted from representative bacteriophages (T3 and ϕX174) in samples augmented with chloride. Herein, chloride enhances FAC reactivity toward dsDNA and, to a lesser extent, toward ssDNA, especially at pH < 7.5. The enhanced reactivity can be attributed to the formation of Cl₂. Second-order rate constants were determined for reactions of ssDNA and dsDNA with HOCl and Cl₂. DNA chlorination kinetics followed the reactivity-selectivity principle, where the more-reactive nucleophilic species (ssDNA, ∼100× more reactive than dsDNA) reacted less selectively with electrophilic FAC species. The addition of chloride was also shown to enhance the inactivation of bacteriophage T3 (dsDNA genome) by FAC but did not enhance the inactivation of bacteriophage ϕX174 (ssDNA genome). Overall, the results suggest that Cl₂ is an important chlorinating agent of nucleic acids and viruses.

Genotype-dependent kinetics of enterovirus inactivation by free chlorine and ultraviolet (UV) irradiation

Inactivation kinetics of enterovirus by disinfection is often studied using a single laboratory strain of a given genotype. Environmental variants of enterovirus are genetically distinct from the corresponding laboratory strain, yet it is poorly understood how these genetic differences affect inactivation. Here we evaluated the inactivation kinetics of nine coxsackievirus B3 (CVB3), ten coxsackievirus B4 (CVB4), and two echovirus 11 (E11) variants by free chlorine and ultraviolet irradiation (UV). The inactivation kinetics by free chlorine were genotype- (i.e., susceptibility: CVB5 < CVB3 ≈ CVB4 < E11) and genogroup-dependent and exhibited up to 15-fold difference among the tested viruses. In contrast, only minor (up to 1.3-fold) differences were observed in the UV inactivation kinetics. The differences in variability between the two disinfectants could be rationalized by their respective inactivation mechanisms: inactivation by UV mainly depends on the genomic size and composition, which was similar for all viruses tested, whereas free chlorine targets the viral capsid protein, which exhibited critical differences between genogroups and genotypes. Finally, we integrated the observed variability in inactivation rate constants into an expanded Chick-Watson model to estimate the overall inactivation of an enterovirus consortium. The results highlight that the distribution of inactivation rate constants and the abundance of each genotype are essential parameters to accurately predict the overall inactivation of an enterovirus population by free chlorine. We conclude that predictions based on inactivation data of a single variant or reference pathogen alone likely overestimate the true disinfection efficiency of free chlorine.