Detection of oxidative damages on viral capsid protein for evaluating structural integrity and infectivity of human norovirus

Identification of human astrovirus genome-linked protein (VPg) essential for virus infectivity

Viral genome-linked proteins (VPgs) have been identified in several single-stranded positive-sense RNA virus families. The presence of such protein in the family Astroviridae has not been fully elucidated, although a putative VPg coding region in open reading frame 1a (ORF1a) of astrovirus with high amino acid sequence similarity to the VPg coding region of Caliciviridae has been previously identified. In this work we present several experimental findings that show that human astrovirus (HAstV) RNA encodes a VPg essential for viral infectivity: (i) RNase treatment of RNA purified from astrovirus-infected cells results in a single protein of 13 to 15 kDa, compatible with the predicted astrovirus VPg size; (ii) the antibody used to detect this 13- to 15-kDa protein is specifically directed against a region that includes the putative VPg coding region; (iii) the 13- to 15-kDa protein detected has been partially sequenced and the sequence obtained is contained in the computationally predicted VPg; (iv) the protein resulting from this putative VPg coding region is a highly disordered protein, resembling the VPg of sobemo-, calici- and potyviruses; (v) proteolytic treatment of the genomic RNA leads to loss of infectivity; and (vi) mutagenesis of Tyr-693 included in the putative VPg protein is lethal for HAstV replication, which strongly supports its functional role in the covalent link with the viral RNA.

UV radiation induces genome-mediated, site-specific cleavage in viral proteins

Much research has been dedicated to understanding the molecular basis of UV damage to biomolecules, yet many questions remain regarding the specific pathways involved. Here we describe a genome-mediated mechanism that causes site-specific virus protein cleavage upon UV irradiation. Bacteriophage MS2 was disinfected with 254 nm UV, and protein damage was characterized with ESI- and MALDI-based FT-ICR, Orbitrap, and TOF mass spectroscopy. Top-down mass spectrometry of the products identified the backbone cleavage site as Cys46-Ser47 in the virus capsid protein, a location of viral genome-protein interaction. The presence of viral RNA was essential to inducing backbone cleavage. The similar bacteriophage GA did not exhibit site-specific protein cleavage. Based on the major protein fragments identified by accurate mass analysis, a cleavage mechanism is proposed by radical formation. The mechanism involves initial oxidation of the Cys46 side chain followed by hydrogen atom abstraction from Ser47 C(α). Computational protein QM/MM studies confirmed the initial steps of the radical mechanism. Collectively, this study describes a rare incidence of genome-induced protein cleavage without the addition of sensitizers.

Environmental influences on virus-host interactions in an Australian subtropical reservoir

Viral and prokaryotic interactions in freshwaters have been investigated worldwide but there are few temporal studies in the tropics and none in the sub-tropics. In this 10-month study, we examined temporal changes in virus-host interactions and viral life cycles (lytic versus lysogenic) in relation to the prevailing environmental conditions in a subtropical water reservoir (Wivenhoe) in southeast Queensland, Australia. Heterotrophic prokaryotes and picocyanobacteria were positively correlated with concentrations of viruses throughout the study, indicating the presence of both bacteriophages and cyanophages in the reservoir. The percentage of heterotrophic prokaryotes and picocyanobacteria containing intracellular viruses (FVIC) ranged between 0.2% and 2.4% and did not vary significantly over the 10-month study, whereas lysogenic heterotrophic prokaryotes were only detected in the drier months of June and July. Spearman rank correlation analysis showed that the oxidative-reduction potential (ORP) of the water reservoir influenced the concentrations of viruses, heterotrophic prokaryotes and picocyanobacteria significantly, with low ORP offering a favourable environment for these components. There was a negative relationship between FVIC and rainfall suggesting the associated run-off altered virus-host interactions. Overall, our study provides novel information and inferences on how virus-host interactions in subtropical freshwaters might respond to changes in precipitation predicted to occur with global climate change.

Methods to detect infectious human enteric viruses in environmental water samples

Currently, a wide range of analytical methods is available for virus detection in environmental water samples. Molecular methods such as polymerase chain reaction (PCR) and quantitative real time PCR (qPCR) have the highest sensitivity and specificity to investigate virus contamination in water, so they are the most commonly used in environmental virology. Despite great sensitivity of PCR, the main limitation is the lack of the correlation between the detected viral genome and viral infectivity, which limits conclusions regarding the significance for public health. To provide information about the infectivity of the detected viruses, cultivation on animal cell culture is the gold standard. However, cell culture infectivity assays are laborious, time consuming and costly. Also, not all viruses are able to produce cytopathic effect and viruses such as human noroviruses have no available cell line for propagation. In this brief review, we present a summary and critical evaluation of different approaches that have been recently proposed to overcome limitations of the traditional cell culture assay and PCR assay such as integrated cell culture-PCR, detection of genome integrity, detection of capsid integrity, and measurement of oxidative damages on viral capsid protein. Techniques for rapid detection of infectious viruses such as fluorescence microscopy and automated flow cytometry have also been suggested to assess virus infectivity in water samples.

Norovirus infectivity in humans and persistence in water

To examine the long-term infectivity of human norovirus in water, 13 study subjects were challenged at different time points with groundwater spiked with the prototype human norovirus, Norwalk virus. Norwalk virus spiked in groundwater remained infectious after storage at room temperature in the dark for 61 days (the last time point tested). The Norwalk virus-seeded groundwater was stored for 1,266 days and analyzed, after RNase treatment, by reverse transcription-quantitative PCR (RT-qPCR) to detect Norwalk virus RNA contained within intact capsids. Norwalk virus RNA within intact capsids was detected in groundwater for 1,266 days, with no significant log(10) reduction throughout 427 days and a significant 1.10-log(10) reduction by day 1266. Purified Norwalk virus RNA (extracted from Norwalk virus virions) persisted for 14 days in groundwater, tap water, and reagent-grade water. This study demonstrates that Norwalk virus in groundwater can remain detectable for over 3 years and can remain infectious for at least 61 days. (ClinicalTrials.gov identifier NCT00313404.).

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.

Chlorine inactivation of human norovirus, murine norovirus and poliovirus in drinking water

AIMS

To evaluate the reduction of human norovirus (HuNoV) by chlorine disinfection under typical drinking water treatment conditions.

METHODS AND RESULTS

HuNoV, murine norovirus (MNV) and poliovirus type 1 (PV1) were inoculated into treated water before chlorination, collected from a drinking water treatment plant, and bench-scale free chlorine disinfection experiments were performed for two initial free chlorine concentrations, 0.1 and 0.5 mg l(-1). Inactivation of MNV reached more than 4 log(10) after 120 and 0.5 min contact time to chlorine at the initial free chlorine concentrations of 0.1 and 0.5 mg l(-1), respectively.

CONCLUSIONS

MNV was inactivated faster than PV1, and there was no significant difference in the viral RNA reduction rate between HuNoV and MNV. The results suggest that appropriate water treatment process with chlorination can manage the risk of HuNoV infection via drinking water supply systems.

SIGNIFICANCE AND IMPACT OF THE STUDY

The data obtained in this study would be useful for assessing or managing the risk of HuNoV infections from drinking water exposure.