Characterization of Norovirus and Other Human Enteric Viruses in Sewage and Stool Samples Through Next-Generation Sequencing
This study aimed to optimize a method to identify human enteric viruses in sewage and stool samples using random primed next-generation sequencing. We tested three methods, two employed virus enrichment based on the binding properties of the viral capsid using pig-mucin capture or by selecting viral RNA prior to library preparation through a capture using the SureSelect target enrichment. The third method was based on a non-specific biophysical precipitation with polyethylene glycol. Full genomes of a number of common human enteric viruses including norovirus, rotavirus, husavirus, enterovirus and astrovirus were obtained....
Source: Food and Environmental Virology - August 23, 2019 Category: Virology Source Type: research
Development and Evaluation of a Novel Armored RNA Technology Using Bacteriophage Q β
In this study, we report a novel technology for preparing AR using bacteriophage Q β and compare its stability with AR prepared using the MS2 phage system for packaging norovirus detection target RNA. AR could be successfully and efficiently produced using the developed bacteriophage Qβ system. Two types of AR–AR-QNoV prepared using the Qβ system and AR-MNoV prepared using th e MS2 system—were stored at different temperatures for different durations. After incubating at − 20 °C for 360 days, the copy numbers of AR-QNoV and AR-MNoV decreased by 8.9% and 35.9%, respectively. After incubating at 4 °C for 60 da...
Source: Food and Environmental Virology - August 20, 2019 Category: Virology Source Type: research
Molecular Characterization and Phylogenetic Analysis of Enteroviruses and Hepatitis A Viruses in Sewage Samples, Northern Italy, 2016
This study focused on the molecular characterization and phylogenetic analysis of the EVs and HAVs identified in 33 sewage samples collected every 15 Â days at the influent of a wastewater treatment plant located in Northern Italy from March to October 2016. According to the results of the molecular characterization, the most frequently identified viruses were Echovirus 6 (E-6), E-11 and HAV-IA. The phylogenetic analyses indicated the rapid genet ic evolution of E-6 and E-1; noteworthy, most E-11 strains clustered with a strain isolated from a clinical sample collected in the same geographical area over the same period by ...
Source: Food and Environmental Virology - August 15, 2019 Category: Virology Source Type: research
Evaluation of Human- and Animal-Specific Viral Markers and Application of CrAssphage, Pepper Mild Mottle Virus, and Tobacco Mosaic Virus as Potential Fecal Pollution Markers to River Water in Japan
AbstractFive human-specific markers were detected in 59 –74% of 27 human fecal-source samples collected in Yamanashi Prefecture, Japan. Similarly, potential human-specific markers, crAssphage, pepper mild mottle virus (PMMoV), and tobacco mosaic virus were detected in 96–100% of samples, with crAssphage showing the maximum concentration of 12.03 log copies/L. However, these markers were detected in 100% (3/3) of pig fecal-source samples, suggesting their applicability as general fecal pollution markers. Microbial source tracking analysis demonstrated that the rivers are contaminated by human and pig fecal sources. CrA...
Source: Food and Environmental Virology - August 1, 2019 Category: Virology Source Type: research
Year-Long Rhinovirus Infection is Influenced by Atmospheric Conditions, Outdoor Air Virus Presence, and Immune System-Related Genetic Polymorphisms
AbstractRhinovirus is a common picornavirus with over 150 serotypes and three species, which is responsible for half of the human common cold cases. In people with chronic respiratory conditions and elders, it may also cause life-threatening diseases. Transmission routes are not definitively established but may involve direct human-to-human and indirect transmission (surfaces and aerosols based). In the present study, year-long presence of virus was tested by qPCR in the nostrils of young healthy volunteers and indoor and outdoor air samples. Results were correlated to atmospheric conditions (meteorological and air quality...
Source: Food and Environmental Virology - July 25, 2019 Category: Virology Source Type: research
Molecular Characterization of Coxsackievirus B5 Isolates from Sewage, Italy 2016 –2017
AbstractHereby, the partial Viral Protein 1 sequences of Coxsackievirus B5 (CV-B5) from sewage samples, collected in Italy from 2016 to 2017, were compared with those available in GenBank from clinical samples. Phylogenetic analysis highlighted: (I) the predominant circulation of CV-B5 genogroup B in Italy, and (II) the presence of two new sub-genogroups. (Source: Food and Environmental Virology)
Source: Food and Environmental Virology - July 25, 2019 Category: Virology Source Type: research
Norovirus Monitoring in Oysters Using Two Different Extraction Methods
This study aimed to assess the presence of noroviruses in oysters extracted using a proteinase K extraction (ISO 15216 method) and an adsorption –elution method. Seventy oyster samples were extracted using the two extraction methods and evaluated using RT-nested PCR. The results showed norovirus detection rates at an equal frequency of 28.6%, of which a total of 48 (68.6%) samples had corresponding positive or negative results, while there were 22 (31.4%) samples with discrepant results. Norovirus genogroup (G)I, GII, and mixed GI and GII were detected in 20%, 4.3%, and 4.3% of samples, respectively, by the proteinase K ...
Source: Food and Environmental Virology - July 23, 2019 Category: Virology Source Type: research
Screening and Molecular Characterization of Hepatitis E Virus in Slaughter Pigs in Serbia
This study provides the first analysis of the genetic diver sity and circulation dynamics of HEV in pigs at slaughterhouses in Serbia. (Source: Food and Environmental Virology)
Source: Food and Environmental Virology - June 25, 2019 Category: Virology Source Type: research
Assessment of the Applicability of Capsid-Integrity Assays for Detecting Infectious Norovirus Inactivated by Heat or UV Irradiation
In this study, two such methods (RNase and porcine gastric mucin) which were designed to remove viruses with compromised capsids (and therefore assumed to be non-viable), were assessed for their ability to quantify viable F-specific RNA bacteriophage (FRNAP) and human norovirus following inactivation by UV-C or heat. It was found that while both methods could remove a proportion of non-viable viruses, a large proportion of non-viable virus remained to be detected by RT-qPCR, leading to overestimations of the viable population. A model was then developed to determine the proportion of RT-qPCR detectable RNA from non-viable ...
Source: Food and Environmental Virology - June 4, 2019 Category: Virology Source Type: research
Interlaboratory Comparative Study to Detect Potentially Infectious Human Enteric Viruses in Influent and Effluent Waters
In this study, we evaluated a protocol based on aluminum adsorption –precipitation to concentrate several human enteric viruses, including norovirus genogroup I (NoV GI), NoV GII, hepatitis A virus (HAV), astrovirus (HAstV), and rotavirus (RV), with limits of detection of 4.08, 4.64, 5.46 log genomic copies (gc)/L, 3.31, and 5.41 log PCR units (PCRU)/L, respectiv ely. Furthermore, the method was applied in two independent laboratories to monitor the presence of NoV GI, NoV GII, and HAV in effluent and influent waters collected from five WWTPs at two different sampling dates. Concomitantly, a viability PMAxx-RT-qPCR was ...
Source: Food and Environmental Virology - May 31, 2019 Category: Virology Source Type: research
Surveillance of Enteric Viruses and Thermotolerant Coliforms in Surface Water and Bivalves from a Mangrove Estuary in Southeastern Brazil
This study was conducted to evaluate the microbiological quality of a mangrove estuary in the Vit ória Bay region, EspÃrito Santo, Brazil. We analyzed the presence and concentration of enteric viruses and thermotolerant coliforms in water, mussels (Mytella charruana andMytella guyanensis), and oysters (Crassostrea rhizophorae), collected over a 13-month period. Human adenovirus, rotavirus A (RVA), and norovirus genogroup II were analyzed by quantitative PCR. The highest viral load was found in RVA-positive samples with a concentration of 3.0  × 104 genome copies (GC) L−1 in water samples and 1.3  × 105 GCÂ...
Source: Food and Environmental Virology - May 31, 2019 Category: Virology Source Type: research
Use of F-Specific RNA Bacteriophage to Estimate Infectious Norovirus Levels in Oysters
In this study, we investigated the relationships between F-RNA phage and norovirus in digestive tissues from two sets of oyster samples, one randomly collected at retail (630 samples), and one linked to suspected norovirus illness outbreaks (nine samples). A positive association and correlation between PCR-detectable levels of genogroup II F-RNA bacteriophage (associated with human faecal contamination) and norovirus was found in both sets of samples, with more samples positive for genogroup II phage, at generally higher levels than norovirus. Levels of both viruses were higher in outbreak-related than retail samples. Infe...
Source: Food and Environmental Virology - May 20, 2019 Category: Virology Source Type: research
Performance Evaluation of Human-Specific Viral Markers and Application of Pepper Mild Mottle Virus and CrAssphage to Environmental Water Samples as Fecal Pollution Markers in the Kathmandu Valley, Nepal
AbstractMonitoring of environmental water is crucial to protecting humans and animals from possible health risks. Although numerous human-specific viral markers have been designed to track the presence of human fecal contamination in water, they lack adequate sensitivity and specificity in different geographical regions. We evaluated the performances of six human-specific viral markers [Aichi virus 1 (AiV-1), human adenoviruses (HAdVs), BK and JC polyomaviruses (BKPyVs and JCPyVs), pepper mild mottle virus (PMMoV), and crAssphage] using 122 fecal-source samples collected from humans and five animal hosts in the Kathmandu V...
Source: Food and Environmental Virology - May 12, 2019 Category: Virology Source Type: research
Cold Atmospheric Plasma as a Novel Method for Inactivation of Potato Virus Y in Water Samples
AbstractWhile one of the biggest problems we are facing today is water scarcity, enormous quantities of water are still being used in irrigation. If contaminated, this water can act as an effective pathway for the spread of disease-causing agents, like viruses. Here, we present a novel, environmentally friendly method known as cold atmospheric plasma for inactivation of viruses in water used in closed irrigation systems. We measured the plasma-mediated viral RNA degradation as well as the plasma-induced loss of viral infectivity using potato virus Y as a model virus due to its confirmed water transmissibility and economic ...
Source: Food and Environmental Virology - April 28, 2019 Category: Virology Source Type: research
Missing the Match Might Not Cost You the Game: Primer-Template Mismatches Studied in Different Hepatitis A Virus Variants
AbstractMismatches between template sequences and reverse transcription (RT) or polymerase chain reaction (PCR) primers can lead to underestimation or false negative results during detection and quantification of sequence-diverse viruses. We performed an in silico inclusivity analysis of a widely used RT-PCR assay for detection of hepatitis A virus (HAV) in food, described in ISO 15216-1. One of the most common mismatches found was a single G (primer) to U (template) mismatch located at the terminal 3 ′-end of the reverse primer region. This mismatch was present in all genotype III sequences available in GenBank. Partial...
Source: Food and Environmental Virology - April 18, 2019 Category: Virology Source Type: research
