Detection of norovirus genogroup IV, klassevirus, and pepper mild mottle virus in sewage samples in South Korea

CrAssphage as an indicator of human-fecal contamination in water environment and virus reduction in wastewater treatment

Viral indicators of human-fecal contamination in wastewaters and environmental waters have been getting much attention in the past decade. Cross-assembly phage (crAssphage) is the most abundant DNA virus in human feces. Recently, the usefulness of crAssphage as a microbial source tracking and water quality monitoring tool for human-fecal contamination has been highlighted. Here, we conducted a comprehensive review on crAssphage in water, focusing on detection methodology, concentration range in various waters and wastewaters, specificity to human-fecal contamination, and reduction in wastewater treatment systems. This review highlights that crAssphage is globally distributed in wastewaters and various fecal-contaminated water bodies at high concentrations without seasonal fluctuations. CrAssphage is highly specific to human-fecal contamination and is rarely found in animal feces. It also has a good potential as a performance indicator to ensure virus reduction in wastewater treatment systems. Accordingly, crAssphage could be an effective tool for monitoring of human-fecal contamination and potential presence of fecal pathogenic microbes in environmental waters. Bridging the research gaps highlighted in this review would make crAssphage a powerful tool to support the control of water-related health risks.

Back-estimation of norovirus infections through wastewater-based epidemiology: A systematic review and parameter sensitivity

The amount of norovirus RNA (Ribonucleic Acid) in raw wastewater, collected from a wastewater treatment plant (WWTP), can provide an indication of disease prevalence within the sampled catchment. However, an accurate back-estimation might be impeded by the uncertainties from in-sewer/in-sample degradation of viral RNA, variable shedding magnitude, and difficulties in measurement within raw wastewater. The current study reviewed the published literature regarding the factors of norovirus shedding, viral RNA decay in wastewater, and the occurrence of norovirus RNA in raw wastewater based on molecular detection. Sensitivity analysis for WBE back-estimation was conducted using the reported data of the factors mentioned above considering different viral loads in wastewater samples. It was found that the back-estimation is more sensitive to analytical detection uncertainty than shedding variability for norovirus. Although seasonal temperature change can lead to variation of decay rates and may influence the sensitivity of this pathogen-specific parameter, decay rates of norovirus RNA contribute negligibly to the variance in estimating disease prevalence, based on the available data from decay experiments in bulk wastewater under different temperatures. However, the effects of in-sewer transportation on viral RNA decay and retardation by sewer biofilms on pipe surfaces are largely unknown. Given the highest uncertainty from analytical measurement by molecular methods and complexity of in-sewer processes that norovirus experienced during the transportation to WWTP, future investigations are encouraged to improve the accuracy of viral RNA detection in wastewater and delineate viral retardation/interactions with wastewater biofilms in real sewers.

Norovirus detection in wastewater and its correlation with human gastroenteritis: a systematic review and meta-analysis

Norovirus (NoV) is a major cause of sporadic cases and outbreaks of acute gastroenteritis (AGE), thereby imposing threat to health globally. It is unclear how quantitation of wastewater NoV reflects the incidence of human AGE infections; therefore, we conducted this systematic review and meta-analysis of published NoV wastewater surveillance studies. A literature search was performed, and all studies on NoV wastewater surveillance were identified. Quantitative results were evaluated. The results showed that the overall detection rate of NoV in wastewater was 82.10% (95% confidence interval [CI]: 74.22-89.92%); NoV concentration was statistically significant in terms of season (P < 0.001), with higher concentration in spring and winter. There were positive correlations between NoV GII concentration in wastewater and GII AGE cases (rs = 0.51, 95% CI: 0.18-0.74, I2 = 0%), total AGE cases (rs = 0.40, 95% CI: 0.15-0.61, I2 = 23%) and NoV outbreaks (rs = 0.47, 95% CI: 0.30-0.62, I2 = 0%). Results of cross-correlation analysis of partial data indicated that variations in GII concentration were consistent with or ahead of those in the number of AGE cases. The diversity of NoV genotypes in wastewater was elucidated, and the dominant strains in wastewater showed a consistent temporal distribution with those responsible for human AGE. Our study demonstrated the potential association of NoV detected in wastewater with AGE infections, and further studies are needed to confirm this conclusion.

Proposed approaches for coronaviruses elimination from wastewater: Membrane techniques and nanotechnology solutions

Since the beginning of the third Millennium, specifically during the last 18 years, three outbreaks of diseases have been recorded caused by coronaviruses (CoVs). The latest outbreak of these diseases was Coronavirus Disease 2019 (COVID-19), which has been declared by the World Health Organization (WHO) as a pandemic. For this reason, current efforts of the environmental, epidemiology scientists, engineers, and water sector professionals are ongoing to detect CoV in environmental components, especially water, and assess the relative risk of exposure to these systems and any measures needed to protect the public health, workers, and public, in general. This review presents a brief overview of CoV in water, wastewater, and surface water based on a literature search providing different solutions to keep water protected from CoV. Membrane techniques are very attractive solutions for virus elimination in water. In addition, another essential solution is nanotechnology and its applications in the detection and protection of human and water systems.

Pepper Mild Mottle Virus as Indicator of Pollution: Assessment of Prevalence and Concentration in Different Water Environments in Italy

Pepper mild mottle virus (PMMoV), a plant pathogenic virus belonging to the family Virgoviridae, has been proposed as a potential viral indicator for human faecal pollution in aquatic environments. The present study investigated the occurrence, amount and diversity of PMMoV in water environments in Italy. A total of 254 water samples, collected between 2017 and 2019 from different types of water, were analysed. In detail, 92 raw sewage, 32 treated sewage, 16 river samples, 9 estuarine waters, 20 bathing waters, 67 groundwater samples and 18 drinking waters were tested. PMMoV was detected in 79% and 75% of untreated and treated sewage samples, respectively, 75% of river samples, 67% and 25% of estuarine and bathing waters and 13% of groundwater samples. No positive was detected in drinking water. The geometric mean of viral concentrations (genome copies/L) was ranked as follows: raw sewage (2.2 × 10⁶) > treated sewage (2.9 × 10⁵) > river waters (6.1 × 10²) > estuarine waters (4.8 × 10²) > bathing waters (8.5 × 10¹) > groundwater (5.9 × 10¹). A statistically significant variation of viral loads could be observed between raw and treated sewage and between these and all the other water matrices. PMMoV occurrence and viral loads did not display seasonal variation in raw sewage nor correlation with faecal indicator bacteria in marine waters and groundwater. This study represents the first report on the occurrence and quantification PMMoV in different water environments in Italy. Further studies are required to evaluate the suitability of PMMoV as a viral indicator for human faecal pollution and for viral pathogens in waters.

Hygiene risk of waterborne pathogenic viruses in rural communities using onsite sanitation systems and shallow dug wells

We evaluated the hygienic influence of onsite sanitation systems (OSSs) on drinking water wells in rural Sri Lanka by determining the safe setback distance between wells and the management of OSSs. Although previous studies have used bacterial indicators such as E. coli to evaluate the OSS impact, these parameters cannot assess the hygiene risk for waterborne pathogenic viruses (e.g. rotaviruses). Therefore, pepper mild mottle virus was selected as an indicator of human-specific faecal virus contamination. From a viral perspective, not only can the horizontal distance between a well and the nearest OSS reasonably represent hygiene safety, but the OSS sludge management can mitigate the contamination of wells even at short distances from the OSSs. Quantitative microbial risk assessment suggests that the infection risk of rotavirus was extremely high compared to the international standard. As proper management of OSSs would be key to reducing viral risk, it is necessary to reach out to the residents who are unaware of the importance and necessity of such management.

Molecular Detection of Human Salivirus in Italy Through Monitoring of Urban Sewages

Salivirus (SalV) is a newly discovered virus associated to acute gastroenteritis in humans. In Italy, its prevalence and genetic diversity is unknown. To reduce this knowledge gap, 124 sewage samples collected throughout the country were analyzed for SalV by two nested RT-PCRs targeting the 5'UTR and the 3D regions and by real-time RT-qPCR. Virus RNA was detected in 37 (29.8%) samples; of these, 24 could be characterized and all belonged to genotype A1. Viral concentrations ranged between 2.8 × 10³ and 1.9 × 10⁵ genome copies per liter. This is the first report of SalV occurrence in water environments in Italy, suggesting that SalV infection is not uncommon in this country.

Norovirus Seroprevalence among Adults in the United States: Analysis of NHANES Serum Specimens from 1999-2000 and 2003-2004

Norovirus is the most common cause of epidemic and endemic acute gastroenteritis. However, national estimates of the infection burden are challenging. This study used a nationally representative serum bank to estimate the seroprevalence to five norovirus genotypes including three GII variants: GI.1 Norwalk, GI.4, GII.3, GII.4 US95/96, GII.4 Farmington Hills, GII.4 New Orleans, and GIV.1 in the USA population (aged 16 to 49 years). Changes in seroprevalence to the three norovirus GII.4 variants between 1999 and 2000, as well as 2003 and 2004, were measured to examine the role of population immunity in the emergence of pandemic GII.4 noroviruses. The overall population-adjusted seroprevalence to any norovirus was 90.0% (1999 to 2000) and 95.9% (2003 to 2004). Seroprevalence was highest to GI.1 Norwalk, GII.3, and the three GII.4 noroviruses. Seroprevalence to GII.4 Farmington Hills increased significantly between the 1999 and 2000, as well as the 2003 and 2004, study cycles, consistent with the emergence of this pandemic strain. Seroprevalence to GII.4 New Orleans also increased over time, but to a lesser degree. Antibodies against the GIV.1 norovirus were consistently detected (population-adjusted seroprevalence 19.1% to 25.9%), with rates increasing with age. This study confirms the high burden of norovirus infection in US adults, with most adults having multiple norovirus infections over their lifetime.

Pepper mild mottle virus: A plant pathogen with a greater purpose in (waste)water treatment development and public health management

An enteric virus surrogate and reliable domestic wastewater tracer is needed to manage microbial quality of food and water as (waste)water reuse becomes more prevalent in response to population growth, urbanization, and climate change. Pepper mild mottle virus (PMMoV), a plant pathogen found at high concentrations in domestic wastewater, is a promising surrogate for enteric viruses that has been incorporated into over 29 water- and food-related microbial quality and technology investigations around the world. This review consolidates the available literature from across disciplines to provide guidance on the utility of PMMoV as either an enteric virus surrogate and/or domestic wastewater marker in various situations. Synthesis of the available research supports PMMoV as a useful enteric virus process indicator since its high concentrations in source water allow for identifying the extent of virus log-reductions in field, pilot, and full-scale (waste)water treatment systems. PMMoV reduction levels during many forms of wastewater treatment were less than or equal to the reduction of other viruses, suggesting this virus can serve as an enteric virus surrogate when evaluating new treatment technologies. PMMoV excels as an index virus for enteric viruses in environmental waters exposed to untreated domestic wastewater because it was detected more frequently and in higher concentrations than other human viruses in groundwater (72.2%) and surface waters (freshwater, 94.5% and coastal, 72.2%), with pathogen co-detection rates as high as 72.3%. Additionally, PMMoV is an important microbial source tracking marker, most appropriately associated with untreated domestic wastewater, where its pooled-specificity is 90% and pooled-sensitivity is 100%, as opposed to human feces where its pooled-sensitivity is only 11.3%. A limited number of studies have also suggested that PMMoV may be a useful index virus for enteric viruses in monitoring the microbial quality of fresh produce and shellfish, but further research is needed on these topics. Finally, future work is needed to fill in knowledge gaps regarding PMMoV's global specificity and sensitivity.

Detection of Pathogenic Viruses in the Ambient Air in Seoul, Korea

The possible transport of pathogenic microorganisms during Asian dust events could be an important concern for health workers; however, this is still uncertain owing to a lack of supporting evidence. The present study aimed to investigate the presence of pathogenic microorganisms in air samples collected during the Asian and non-Asian dust periods. Between March and September 2016, air samples were collected at three weather observation stations in Seoul using a high-volume air sampler. Multiplex PCR was performed using the Allplex™ respiratory and gastrointestinal panel assay kits to detect 46 microorganisms. RT-PCR was performed for klassevirus, Aichivirus, and human parechovirus (HPeV) detection. In total, 71 air samples were collected during the Asian (8 samples) and non-Asian (63 samples) dust events. During an Asian dust event, only one human rhinovirus (HRV)-positive air sample was collected on April 23. During the non-Asian dust period, HRV, HPeV, norovirus (NoV), enteroaggregative Escherichia coli (EAEC), enterotoxigenic E. coli (ETEC), and Blastocystis hominis were detected in four, two, one, one, one, and one air samples, respectively. Pathogenic viruses were mostly detected in ambient air samples during the non-Asian dust period, which suggests a possible air-borne transmission of viral pathogens; however, the role of Asian dust in epidemics caused by pathogenic viruses is unclear.

Distribution of Naturally Occurring Norovirus Genogroups I, II, and IV in Oyster Tissues

This study evaluated different tissues of naturally contaminated oysters (Crassostrea belcheri) for the presence of noroviruses. RNA from digestive tissues, gills, and mantle of the oysters was extracted and tested for norovirus genogroup (G) I, GII, and GIV using RT-nested PCR. In spiking experiments with a known norovirus, GII.4, the detection limits were 2.97 × 10² RNA copies/g of digestive tissues, 2.62 × 10² RNA copies/g of gills, and 1.61 × 10³ RNA copies/g of mantle. A total of 85 oyster samples were collected from a fresh market in Bangkok, Thailand. Noroviruses were found in the oyster samples (40/85, 47%): GI (29/85, 34.1%), GII (9/85, 10.5%), mixed GI and GII (1/85, 1.2%), and GIV (1/85, 1.2%). All three genogroups were found in the digestive tissues of oysters. Norovirus GI was present in all three tissues with the highest frequency in the mantle, and was additionally detected in multiple tissues in some oysters. GII was also detected in all three tissues, but was not detected in multiple tissues in the same oyster. For genogroup I, only GI.2 could be identified and it was found in all tissues. For genogroup II, three different genotypes were identified, namely GII.4 which was detected in the gills and the mantle, GII.17 which was detected in the digestive tissues, and GII.21 which was detected in the mantle. GIV.1 was identified in the digestive tissues of one oyster. This is the first report on the presence of human GIV.1 in oyster in Thailand, and the results indicate oyster as a possible vehicle for transmission of all norovirus genogroups in Thailand.

Cellulose-based virus-retentive filters: a review

Viral filtration is a critical step in the purification of biologics and in the monitoring of microbiological water quality. Viral filters are also essential protection elements against airborne viral particles. The present review first focuses on cellulose-based filter media currently used for size-exclusion and/or adsorptive filtration of viruses from biopharmaceutical and environmental water samples. Data from spiking studies quantifying the viral filtration performance of cellulosic filters are detailed, i.e., first, the virus reduction capacity of regenerated cellulose hollow fiber filters in the manufacturing process of blood products and, second, the efficiency of virus recovery/concentration from water samples by the viradel (virus adsorption-elution) method using charge modified, electropositive cellulosic filters or conventional electronegative cellulose ester microfilters. Viral analysis of field water samples by the viradel technique is also surveyed. This review then describes cellulose-based filter media used in individual protection equipment against airborne viral pathogens, presenting innovative filtration media with virucidal properties. Some pros and cons of cellulosic viral filters and perspectives for cellulose-based materials in viral filtration are underlined in the review.

Saliviruses-the first knowledge about a newly discovered human picornavirus

The salivirus, first discovered in the year 2009, is a member of the large and growing family Picornaviridae. At present, the genus Salivirus contains 1 species Salivirus A and 2 genotypes, Salivirus A1 and Salivirus A2. Salivirus has been identified in humans and chimpanzees and may cause acute gastroenteritis in humans, having been detected in 0% to 8.7% of fecal samples collected from gastroenteritis in different human populations. Salivirus is ubiquitous in wastewater of human origin and river water specimens worldwide and represents a potential indicator human RNA virus for monitoring of environmental samples. This review summarizes the current knowledge on saliviruses including discovery, taxonomy, genome structure, and genetic diversity; covers all aspects of infection including epidemiology, molecular epidemiology, clinical feature, host species, environmental characteristics, and laboratory diagnosis; and gives a summary of possible future perspectives.

Genetically distinct genogroup IV norovirus strains identified in wastewater

We investigated the prevalence and genetic diversity of genogroup IV norovirus (GIV NoV) strains in wastewater in Arizona, United States, over a 13-month period. Among 50 wastewater samples tested, GIV NoVs were identified in 13 (26 %) of the samples. A total of 47 different GIV NoV strains were identified, which were classified into two genetically distinct clusters: the GIV.1 human cluster and a unique genetic cluster closely related to strains previously identified in Japanese wastewater. The results provide additional evidence of the considerable genetic diversity among GIV NoV strains through the analysis of wastewater containing virus strains shed from all populations.

Occurrence of Norovirus GIV in Environmental Water Samples from Belém City, Amazon Region, Brazil

Noroviruses are the major cause of non-bacterial acute gastroenteritis outbreaks in humans, with few reports about the occurrence of the norovirus GIV strain. We investigated the presence of norovirus GIV in surface water (river, bay, and stream) and untreated sewage, and we determined a positivity rate of 9.4% (9/96). The strains genotyped were GIV.1. To our knowledge, this is the first report of GIV in Brazil.

A novel feline norovirus in diarrheic cats

By screening a collection of fecal samples from young cats housed in three different shelters in South Italy, noroviruses (NoVs) were found in 3/48 (6.2%) specimens of animals with enteritis signs while they were not detected in samples collected from healthy cats (0/57). Upon sequence analysis of the short RNA-dependent RNA polymerase (RdRp) region, the three strains displayed the highest nucleotide (nt) and amino acid (aa) identities to the prototype GIV.2 strain lion/Pistoia/387/06/ITA (91.0–93.0% nt and 97.0–98.0% aa). The sequence of ~ 3.4-kb portion at the 3′ end of the genome of a NoV strain, TE/77-13/ITA, was determined. In the full-length ORF2, encoding the VP1 capsid protein, the virus was genetically closest to the canine GVI.2 NoV strains C33/Viseu/2007/PRT and FD53/2007/ITA (81.0–84.0% nt and 93.0–94.0% aa identities), suggesting a recombination nature, with the cross-over site being mapped to the ORF1-ORF2 junction. Based on the full-length VP1 amino acid sequence, we classified the novel feline NoV, together with the canine strains Viseu and FD53, as a genotype 2, within the genogroup GVI. These findings indicate that, as observed for GIV NoV, GVI strains may infect both the canine and feline host. Unrestricted circulation of NoV strains in small carnivores may provide the basis for quick genetic diversification of these viruses by recombination. Interspecies circulation of NoVs in pets must also be considered when facing outbreaks of enteric diseases in these animals.

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GIV and GVI NoVs have been recently found in domestic carnivores.

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In this study, NoV strains resembling animal GIV.2 NoVs in their polymerase region were detected in diarrheic cats.

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One Italian strain, TE/77-13/ITA, in the full-length VP1 sequence shared the highest identity to the canine GVI.2 NoVs.

Detection of pepper mild mottle virus in pepper sauce in China

Pepper mild mottle virus (PMMoV) was detected by RT-PCR in all 42 pepper sauce samples from the 10 main manufacturing provinces in China at concentrations ranging from 3.8 to 8.8 (Log10 copies/mL). Their coat protein nucleotide sequences had 97.4 to 100 % identity to each other and 92.4 to 100 % to other published isolates. The samples remained infectious to N. benthamiana, indicating that commercial trade in sauce could contribute to the natural spread of PMMoV.

Development of enhanced primer sets for detection of norovirus

Norovirus (NV) is a major viral pathogen that causes nonbacterial acute gastroenteritis and outbreaks of food-borne disease. The genotype of NV most frequently responsible for NV outbreaks is GII.4, which accounts for 60–80% of cases. Moreover, original and new NV variant types have been continuously emerging, and their emergence is related to the recent global increase in NV infection. In this study, we developed advanced primer sets (NKI-F/R/F2, NKII-F/R/R2) for the detection of NV, including the variant types. The new primer sets were compared with conventional primer sets (GI-F1/R1/F2, SRI-1/2/3, GII-F1/R1/F2, and SRII-1/2/3) to evaluate their efficiency when using clinical and environmental samples. Using reverse transcription polymerase chain reaction (RT-PCR) and seminested PCR, NV GI and GII were detected in 91.7% (NKI-F/R/F2), 89.3% (NKII-F/R/R2), 54.2% (GI-F1/R1/F2), 52.5% (GII-F1/R1/F2), 25.0% (SRI-1/2/3), and 32.2% (SRII-1/2/3) of clinical and environmental specimens. Therefore, our primer sets perform better than conventional primer sets in the detection of emerged types of NV and could be used in the future for epidemiological diagnosis of infection with the virus.

Environmental surveillance for human astrovirus in Shandong Province, China in 2013

Human astroviruses (HAstVs) are one of the leading viral agents of acute gastroenteritis. However, there is limited information on HAstVs in China. Here, we describe the molecular characterization of HAstVs in Shandong, China via sewage surveillance. A total of 23 sewage samples were collected from sewage treatment plants in the cities of Jinan and Linyi in 2013. After concentration via adsorption-elution method, 9 samples (39.1%) were positive by reverse transcription PCR (RT-PCR) for the presence of the 719-nt HAstV nucleotide sequence. Genetic cloning and sequencing were performed on positive PCR products, and 26 HAstV sequences were obtained. Phylogenetic analysis on these sequences revealed 4 genotypes (HAstV-1, -2, -4 and -5), with HAstV-1 and -5 as the most common genotypes in Jinan and Linyi, respectively. Homologous comparison revealed Shandong sequences had relatively less genetic divergence among themselves than with foreign sequences. This study represents the first effort to investigate the genotypes and molecular epidemiology of HAstVs via sewage surveillance in China. The high detection rate in this study reflects that HAstVs circulated at a relatively high frequency in the local population, and demonstrates that environmental surveillance is an effective method in investigating circulating HAstVs.

Quantification and genetic analysis of salivirus/klassevirus in wastewater in Arizona, USA

Salivirus/klassevirus sequences were identified in 7 (15%) wastewater samples collected in Arizona monthly for a year, with the highest concentration of 2.28 × 10(5) and 2.46 × 10(4) copies/L in influent and effluent, respectively. This is the first report of quantification and genetic analysis of salivirus/klassevirus in water samples in the United States.