Early Days of Food and Environmental Virology

Impact of sample clarification by size exclusion on virus detection and diversity in wastewater-based epidemiology

The use of wastewater-based epidemiology (WBE) for early detection of virus circulation and response during the SARS-CoV-2 pandemic increased interest in and use of virus concentration protocols that are quick, scalable, and efficient. One such protocol involves sample clarification by size fractionation using either low-speed centrifugation to produce a clarified supernatant or membrane filtration to produce an initial filtrate depleted of solids, eukaryotes and bacterial present in wastewater (WW), followed by concentration of virus particles by ultrafiltration of the above. While this approach has been successful in identifying viruses from WW, it assumes that majority of the viruses of interest should be present in the fraction obtained by ultrafiltration of the initial filtrate, with negligible loss of viral particles and viral diversity. We used WW samples collected in a population of ~700,000 in southwest USA between October 2019 and March 2021, targeting three non-enveloped viruses (enteroviruses [EV], canine picornaviruses [CanPV], and human adenovirus 41 [Ad41]), to evaluate whether size fractionation of WW prior to ultrafiltration leads to appreciable differences in the virus presence and diversity determined. We showed that virus presence or absence in WW samples in both portions (filter trapped solids [FTS] and filtrate) are not consistent with each other. We also found that in cases where virus was detected in both fractions, virus diversity (or types) captured either in FTS or filtrate were not consistent with each other. Hence, preferring one fraction of WW over the other can undermine the capacity of WBE to function as an early warning system and negatively impact the accurate representation of virus presence and diversity in a population.

Novel opportunities for NGS-based one health surveillance of foodborne viruses

Foodborne viral infections rank among the top 5 causes of disease, with noroviruses and hepatitis A causing the greatest burden globally. Contamination of foods by infected food handlers or through environmental pollution are the main sources of foodborne illness, with a lesser role for consumption of products from infected animals. Viral partial genomic sequencing has been used for more than two decades to track foodborne outbreaks and whole genome or metagenomics next-generation-sequencing (NGS) are new additions to the toolbox of food microbiology laboratories. We discuss developments in the field of targeted and metagenomic NGS, with an emphasis on application in food virology, the challenges and possible solutions towards future routine application.

Presence of bacteroidales as a predicator of human enteric viruses in Haihe River of Tianjin City, China

Traditional microbe indicators including total bacteria, total coliforms, fecal coliforms, Escherichia coli, enterococci, and F+ coliphage are all frequently used to characterize the microbial contamination state of water bodies for their correlation with pathogenic bacteria. However, these indicators have a poor relationship with viruses, which pose serious threat to economic and human health. Alternative indicators such as bacteroidales may be suitable complementary alternatives to traditional microbe indicators and are being increasingly reported. In the present study, water was analyzed for selected sites along Haihe River in Tianjin for traditional indicators, an alternative indicator (bacteroidales), pathogenic bacteria (Salmonella, Escherichia coli (E. coli) O157:H7, and Vibrio parahaemolyticus), viruses (enteric adenovirus, norovirus, enterovirus, poliovirus and rotavirus), and physicochemical parameters. Results indicated that traditional microbe indicators detected in this study showed good correlation with pathogenic bacteria, and the alternative indicator (bacteroidales) had a surprisingly good relationship with viral presence. We propose that bacteroidales might be a suitable complementary indicator for viral contamination in water bodies.

Viral Contamination of Food

A review of the relevant foodborne viruses is presented. Published data from scientific journals as well as the data presented in official reports and published on the Internet were used for this review. In the review, information is given for the main foodborne viruses, implicated virus species, and food matrices involved, some history data are given, as well as modes of transmission, and sources of the virus presence in food. Results of surveys on the presence of viruses in different kind of foods commodities (fresh produces and shellfish) and in some cases connections to caused outbreaks are presented. Also, possible zoonotic infection and implicated viruses that could be transmitted through food are given. Human Norovirus followed by hepatitis A virus are the most common foodborne viruses, which are transmitted by food consumed raw, such as shellfish, fresh vegetables, and berry fruit. In developed countries, hepatitis E virus is increasingly being recognized as an emerging viral foodborne pathogen that includes zoonotic transmission via pork products. The existing knowledge gaps and the major future expectations in the detection and surveillance of foodborne viruses are mentioned.

Antiviral Potential of Selected Starter Cultures, Bacteriocins and D,L-Lactic Acid

The antiviral potential of selected bacteria species [lactic acid bacteria (LAB) and micrococcaceae] was examined. By this, the effect of their cell-free supernatants as well as of certain species-related metabolites (sakacin A, nisin, and lactic acid) was investigated on different viruses after exposure at 24 °C for 3 days. Viruses were incubated with supernatants and metabolites in a dilution ratio of 1:10. Data for antiviral effects towards murine norovirus S99 (MNV), influenza A virus A/WSN/33 (H1N1), Newcastle disease virus Montana (NDV) and feline herpesvirus KS 285 (FHV) were generated in vitro simulating pH and temperature conditions according to raw sausage fermentations. Investigations showed no antiviral effect of sakacin A and nisin on MNV, H1N1, FHV and NDV. Furthermore, the antiviral potential of D,L-lactic acid was determined for MNV and H1N1. At raw sausage-related pH values (5.0-6.2) it could be shown that the virus titre for MNV and H1N1 was reduced by a maximum of 3.25 log and 2.5 log units, respectively. In addition, 29 culture supernatants of different bacteria species, mainly LAB and staphylococci, were tested for their antiviral activity against MNV. Only the cell-free supernatant of a Lb. curvatus strain showed a higher virus titre reduction of MNV by 1.25 log units compared to the control. Further studies on the characterisation of this cell-free supernatant were carried out, however, the antiviral substance could not be identified so far.

Multilocus genetic characterization of two ant vectors (Group II "Dirty 22" species) known to contaminate food and food products and spread foodborne pathogens

The U.S. Food and Drug Administration utilizes the presence of filth and extraneous materials as one of the criteria for implementing regulatory actions and assessing adulteration of food products of public health importance. Twenty-two prevalent pest species (also known as the ''Dirty 22'' species) have been considered by this agency as possible vehicles for the spread of foodborne diseases, and the presence of these species is considered an indicator of unsanitary conditions in food processing and storage facilities. In a previous study, we further categorized the Dirty 22 species into four groups: group I includes four cockroach species, group II includes two ant species, group III includes 12 fly species, and group IV includes four rodent species. Here, we describe the development of three nested PCR primer sets and multilocus genetic characterization by amplifying the small subunit rRNA, elongation factor 1-alpha, and wingless (WNT-1) genes of group II Dirty 22 ant species Monomorium pharaonis and Solenopsis molesta. These novel group II Dirty 22 species-specific nested PCR primer sets can be used when the specimens cannot be identified using conventional microscopic methods. These newly developed assays will provide correct identification of group II Dirty 22 ant species, and the information can be used in the control of foodborne pathogens.

Temperature and density dependent induction of a cytopathic effect following infection with non-cytopathic HAV strains

Hepatitis A virus infection and growth in cultured cells is protracted, cell-type restricted, and generally not accompanied by the appearance of a cytopathic effect, with the exception of some culture-adapted strains. We demonstrate that the non-cytopathic HAV strain HM175/clone 1 can be induced to exhibit a cytopathic phenotype in both persistently or acutely infected cells under co-dependent conditions of lower incubation temperature (<34°C) and reduced cell density in both monkey (FRhK-4) and human (A549) cells. This phenotype is not virus-strain restricted, as it was also observed in cells infected with HAV strains, HAS-15 and LSH/S. Cytopathic effect was accompanied by rRNA cleavage, indicating activation of the RNase L pathway, viral negative strand synthesis, caspase-3 activation, and apoptosis. The results indicate that a cytopathic phenotype may be present in some HAV strains that can be induced under appropriate conditions, suggesting the potential for development of a plaque assay for this virus.

Development of a PCR-restriction fragment length polymorphism protocol for rapid detection and differentiation of four cockroach vectors (group I "Dirty 22" species) responsible for food contamination and spreading of foodborne pathogens: public health importance

Assessing the adulteration of food products and the presence of filth and extraneous materials is one of the measures that the U.S. Food and Drug Administration (FDA) utilizes in implementing regulatory actions of public health importance. To date, 22 common pest species (also known as the "Dirty 22" species) have been regarded by this agency as the spreaders of foodborne diseases. We have further categorized the Dirty 22 species into four groups: I has four cockroach species, II has two ant species, III has 12 fly species, and IV has four rodent species. The presence of any Dirty 22 species is also considered an indicator of unsanitary conditions in food processing and storage facilities. In this study, we describe the development of a two-step nested PCR protocol to amplify the small subunit ribosomal gene of group I Dirty 22 species that include four cockroach species: Blattella germanica, Blatta orientalis, Periplaneta americana, and Supella longipalpa, along with the development of a PCR-restriction fragment length polymorphism method for rapid detection and differentiation of these violative species. This method will be utilized when the specimen cannot be identified with conventional microscopic taxonomic methods, especially when only small body parts are separated and recovered from food samples for analysis or when these body parts are in a decomposed state. This new PCR-restriction fragment length polymorphism will provide correct identification of group I Dirty 22 species; this information can then be used in regulation and prevention of foodborne pathogens.

In vitro influence of D/L-lactic acid, sodium chloride and sodium nitrite on the infectivity of feline calicivirus and of ECHO virus as potential surrogates for foodborne viruses

The importance of foodborne viruses is increasingly recognized. Thus, the effect of commonly used food preservation methods on the infectivity of viruses is questioned. In this context, we investigated the antiviral properties of D,L-lactic acid, sodium chloride and sodium nitrite by in vitro studies. Two model viruses, Feline Calicivirus (FCV) and Enteric Cytophatic Human Orphan (ECHO) virus, were chosen for this study simulating important foodborne viruses (human noroviruses (NoV) and human enteroviruses, resp.). The model viruses were exposed to different solutions of D,L-lactic acid (0.1-0.4% w/w, pH 6.0-3.2), of sodium chloride (2-20%, w/v) and of sodium nitrite (100, 150 and 200 ppm) at 4 and 20 °C for a maximum of 7 days. Different results were obtained for the two viruses. ECHO virus was highly stable against D,L-lactic acid and sodium chloride when tested under all conditions. On the contrary, FCV showed less stability but was not effectively inactivated when exposed to low acid and high salt conditions at refrigeration temperatures (4 °C). FCV titers decreased more markedly at 20 °C than 4 °C in all experiments. Sodium nitrite did not show any effect on the inactivation of both viruses. The results indicate that acidification, salting or curing maybe insufficient for effective inactivation of foodborne viruses such as NoV or human enteroviruses during food processing. Thus, application of higher temperature during fermentation and ripening processes maybe more effective toward the inactivation kinetics of less stable viruses. Nevertheless, more studies are needed to examine the antiviral properties of these preserving agents on virus survival and inactivation kinetics in the complex food matrix.

High prevalence of enteric viruses in untreated individual drinking water sources and surface water in Slovenia

Waterborne infections have been shown to be important in outbreaks of gastroenteritis throughout the world. Although improved sanitary conditions are being progressively applied, fecal contaminations remain an emerging problem also in developed countries. The aim of our study was to investigate the prevalence of fecal contaminated water sources in Slovenia, including surface waters and groundwater sources throughout the country. In total, 152 water samples were investigated, of which 72 samples represents groundwater from individual wells, 17 samples from public collection supplies and 63 samples from surface stream waters. Two liters of untreated water samples were collected and concentrated by the adsorption/elution technique with positively charged filters followed by an additional ultracentrifugation step. Group A rotaviruses, noroviruses (genogroups I and II) and astroviruses were detected with real-time RT-PCR method in 69 (45.4%) out of 152 samples collected, of which 31/89 (34.8%) drinking water and 38/63 (60.3%) surface water samples were positive for at least one virus tested. In 30.3% of drinking water samples group A rotaviruses were detected (27/89), followed by noroviruses GI (2.2%; 2/89) and astroviruses (2.2%; 2/89). In drinking groundwater samples group A rotaviruses were detected in 27 out of 72 tested samples (37.5%), genogroup I noroviruses in two (2.8%), and human astroviruses in one (1.4%) samples. In surface water samples norovirus genogroup GII was the most frequently detected (41.3%; 26/63), followed by norovirus GI (33.3%; 21/63), human astrovirus (27.0%; 17/63) and group A rotavirus (17.5%; 11/63). Our study demonstrates relatively high percentage of groundwater contamination in Slovenia and, suggests that raw groundwater used as individual drinking water supply may constitute a possible source of enteric virus infections. In the future, testing for enteric viruses should be applied for drinking water sources in waterborne outbreaks.

Investigations on the frequency of norovirus contamination of ready-to-eat food items in Istanbul, Turkey, by using real-time reverse transcription PCR

Investigation of norovirus (NoV) contamination of food items is important because many outbreaks occur after consumption of contaminated shellfish, vegetables, fruits, and water. The frequency of NoV contamination in food items has not previously been investigated in Turkey. The aim of this study was to investigate the frequency of human NoV genogroups (G) I and II in ready-to-eat tomatoes, parsley, green onion, lettuce, mixed salads, and cracked wheat balls. RNA was extracted with the RNeasy Mini Kit, and a real-time reverse transcription (RT) PCR assay was performed using primers specific for NoV GI and GII. Among the 525 samples analyzed, NoV GII was detected in 1 green onion sample and 1 tomato sample by both SYBR Green and TaqMan real-time RT-PCR assays; no GI virus was detected. The Enterobactericaeae and Escherichia coli levels in the NoV-positive green onion were 6.56 and 1.28 log CFU/g, and those in the tomato were 5.55 and 1.30 log CFU/g, respectively. No significant difference in the bacterial levels was found between the NoV-positive and NoV-negative samples. This study is the first in which NoV GII was found in ready-to-eat food collected from Istanbul, Turkey; thus, these foods may be considered a risk to human health. Epidemiological studies and measures to prevent NoV infection should be considered.