Brian M. Pecson

Virus inactivation mechanisms: impact of disinfectants on virus function and structural integrity

Oxidative processes are often harnessed as tools for pathogen disinfection. Although the pathways responsible for bacterial inactivation with various biocides are fairly well understood, virus inactivation mechanisms are often contradictory or equivocal. In this study, we provide a quantitative analysis of the total damage incurred by a model virus (bacteriophage MS2) upon inactivation induced by five common virucidal agents (heat, UV, hypochlorous acid, singlet oxygen, and chlorine dioxide). Each treatment targets one or more virus functions to achieve inactivation: UV, singlet oxygen, and hypochlorous acid treatments generally render the genome nonreplicable, whereas chlorine dioxide and heat inhibit host-cell recognition/binding. Using a combination of quantitative analytical tools, we identified unique patterns of molecular level modifications in the virus proteins or genome that lead to the inhibition of these functions and eventually inactivation. UV and chlorine treatments, for example, cause site-specific capsid protein backbone cleavage that inhibits viral genome injection into the host cell. Combined, these results will aid in developing better methods for combating waterborne and foodborne viral pathogens and further our understanding of the adaptive changes viruses undergo in response to natural and anthropogenic stressors.

Quantitative PCR for determining the infectivity of bacteriophage MS2 upon inactivation by heat, UV-B radiation, and singlet oxygen: advantages and limitations of an enzymatic treatment to reduce false-positive results.

ABSTRACT Health risks posed by waterborne viruses are difficult to assess because it is tedious or impossible to determine the infectivity of many viruses. Recent studies hypothesized that quantitative PCR (qPCR) could selectively quantify infective viruses if preceded by an enzymatic treatment (ET) to reduce confounding false-positive signals. The goal of this study was to determine if ET with qPCR (ET-qPCR) can be used to accurately quantify the infectivity of the human viral surrogate bacteriophage MS2 upon partial inactivation by three treatments (heating at 72°C, singlet oxygen, and UV radiation). Viruses were inactivated in buffered solutions and a lake water sample and assayed with culturing, qPCR, and ET-qPCR. To ensure that inactivating genome damage was fully captured, primer sets that covered the entire coding region were used. The susceptibility of different genome regions and the maximum genomic damage after each inactivating treatment were compared. We found that (i) qPCR alone caused false-positive results for all treatments, (ii) ET-qPCR significantly reduced (up to >5.2 log units) but did not eliminate the false-positive signals, and (iii) the elimination of false-positive signals differed between inactivating treatments. By assaying the whole coding region, we demonstrated that genome damage only partially accounts for virus inactivation. The possibility of achieving complete accordance between culture- and PCR-based assays is therefore called into doubt. Despite these differences, we postulate that ET-qPCR can track infectivity, given that decreases in infectivity were always accompanied by dose-dependent decreases in ET-qPCR signal. By decreasing false-positive signals, ET-qPCR improved the detection of infectivity loss relative to qPCR.

A real-time PCR method for quantifying viable ascaris eggs using the first internally transcribed spacer region of ribosomal DNA.

ABSTRACT Worldwide, 1.4 billion people are infected with the intestinal worm Ascaris lumbricoides. As a result, Ascaris eggs are commonly found in wastewater and sludges. The current microscopy method for detecting viable Ascaris eggs is time- and labor-intensive. The goal of this study was to develop a real-time quantitative PCR (qPCR) method to determine the levels of total and viable Ascaris eggs in laboratory solutions using the first internally transcribed spacer (ITS-1) region of ribosomal DNA (rDNA) and rRNA. ITS-1 rDNA levels were proportional to Ascaris egg cell numbers, increasing as eggs developed from single cells to mature larvae and ultimately reaching a constant level per egg. Treatments causing >99% inactivation (high heat, moderate heat, ammonia, and UV) eliminated this increase in ITS-1 rDNA levels and caused decreases that were dependent on the treatment type. By taking advantage of this difference in ITS-1 rDNA level between viable, larvated eggs and inactivated, single-celled eggs, qPCR results were used to develop inactivation profiles for the different treatments. No statistical difference from the standard microscopy method was found in 75% of the samples (12 of 16). ITS-1 rRNA was detected only in samples containing viable eggs, but the levels were more variable than rDNA levels and ITS-1 rRNA could not be used for quantification. The detection limit of the rDNA-based method was approximately one larvated egg or 90 single-celled eggs; the detection limit for the rRNA-based method was several orders of magnitude higher. The rDNA qPCR method is promising for both research and regulatory applications.

Framework for using quantitative PCR as a nonculture based method to estimate virus infectivity.

Measuring the efficiency of virus disinfection with quantitative PCR (qPCR) has been criticized as inadequate due to the production of false-positive signals. Such a claim, however, presupposes an understanding of the theoretical qPCR response. Many studies have assumed that the loss in qPCR signal upon disinfection should equal the loss in infectivity, without accounting for the fact that qPCR typically assays only a fraction of the viral genome. This study aimed to develop a theoretical framework to relate viral infectivity with genome damage measured by qPCR. The framework quantified damage to the entire genome based on the qPCR amplification of smaller sections, assuming single-hit inactivation and a Poissonian distribution of damage. The framework was tested and modified using UV(254) inactivation studies with bacteriophage MS2 (culturing and qPCR of approximately half the genome). Genome regions showed heterogeneous sensitivities to UV(254) treatment, thus deviating from the assumption of Poissonian damage. We offered two modifications to account for these deviations and confirmed that the qPCR-based framework accurately estimated virus infectivity. This framework offers the potential to monitor the infectivity of viruses that remain nonculturable (norovirus). While developed for UV(254)-inactivated virus, the framework should apply to any disinfection technique that causes inactivation via single genomic lesions.

Fate of the pathogen indicators phage ΦX174 and Ascaris suum eggs during the production of struvite fertilizer from source-separated urine

Human urine has the potential to be a sustainable, locally and continuously available source of nutrients for agriculture. Phosphate can be efficiently recovered from human urine in the form of the mineral struvite (MgNH4PO4·6H2O). However, struvite formation may be coupled with the precipitation of other constituents present in urine including pathogens, pharmaceuticals, and heavy metals. To determine if struvite fertilizer presents a microbiological health risk to producers and end users, we characterized the fate of a human virus surrogate (phage ΦX174) and the eggs of the helminth Ascaris suum during a low-cost struvite recovery process. While the concentration of phages was similar in both the struvite and the urine, Ascaris eggs accumulated within the solid during the precipitation and filtration process. Subsequent air-drying of the struvite filter cake partially inactivated both microorganisms; however, viable Ascaris eggs and infective phages were still detected after several days of drying. The infectivity of both viruses and eggs was affected by the specific struvite drying conditions: higher inactivation generally occurred with increased air temperature and decreased relative humidity. On a log-log scale, phage inactivation increased linearly with decreasing moisture content of the struvite, while Ascaris inactivation occurred only after achieving a minimum moisture threshold. Sunlight exposure did not directly affect the infectivity of phages or Ascaris eggs in struvite cakes, though the resultant rise in temperature accelerated the drying of the struvite cake, which contributed to inactivation.

Subtle differences in virus composition affect disinfection kinetics and mechanisms

ABSTRACT Viral disinfection kinetics have been studied in depth, but the molecular-level inactivation mechanisms are not understood. Consequently, it is difficult to predict the disinfection behavior of nonculturable viruses, even when related, culturable viruses are available. The objective of this work was to determine how small differences in the composition of the viral genome and proteins impact disinfection. To this end, we investigated the inactivation of three related bacteriophages (MS2, fr, and GA) by UV254, singlet oxygen (1O2), free chlorine (FC), and chlorine dioxide (ClO2). Genome damage was quantified by PCR, and protein damage was assessed by quantitative matrix-assisted laser desorption ionization (MALDI) mass spectrometry. ClO2 caused great variability in the inactivation kinetics between viruses and was the only treatment that did not induce genome damage. The inactivation kinetics were similar for all viruses when treated with disinfectants possessing a genome-damaging component (FC, 1O2, and UV254). On the protein level, UV254 subtly damaged MS2 and fr capsid proteins, whereas GAs capsid remained intact. 1O2 oxidized a methionine residue in MS2 but did not affect the other two viruses. In contrast, FC and ClO2 rapidly degraded the capsid proteins of all three viruses. Protein composition alone could not explain the observed degradation trends; instead, molecular dynamics simulations indicated that degradation is dictated by the solvent-accessible surface area of individual amino acids. Finally, despite the similarities of the three viruses investigated, their mode of inactivation by a single disinfectant varied. This explains why closely related viruses can exhibit drastically different inactivation kinetics.

Photoinactivation of virus on iron-oxide coated sand: enhancing inactivation in sunlit waters

Adsorption onto iron oxides can enhance the removal of waterborne viruses in constructed wetlands and soils. If reversible adsorption is not coupled with inactivation, however, infective viruses may be released when changes in solution conditions cause desorption. The goals of this study were to investigate the release of infective bacteriophages MS2 and ΦX174 (two human viral indicators) after adsorption onto an iron oxide coated sand (IOCS), and to promote viral inactivation by exploiting the photoreactive properties of the IOCS. The iron oxide coating greatly enhanced viral adsorption (adsorption densities up to ≈ 10(9) infective viruses/g IOCS) onto the sand, but had no affect on infectivity. Viruses that were adsorbed onto IOCS under control conditions (pH 7.5, 10 mM Tris, 1250 μS/cm) were released into solution in an infective state with increases in pH and humic acid concentrations. The exposure of IOCS-adsorbed MS2 to sunlight irradiation caused significant inactivation via a photocatalytic mechanism in both buffered solutions and in wastewater samples (4.9 log(10) and 3.3 log(10) inactivation after 24-h exposure, respectively). Unlike MS2, ΦX174 inactivation was not enhanced by photocatalysis. In summary, IOCS enhanced the separation of viruses from the water column, and additionally provided a photocatalytic mechanism to promote inactivation of one of the surrogates studied. These qualities make it an attractive option for improving viral control strategies in constructed wetlands.