Eukaryotic viruses in wastewater samples from the United States

Improving viral annotation with artificial intelligence

Viruses of bacteria, "phages," are fundamental, poorly understood components of microbial community structure and function. Additionally, their dependence on hosts for replication positions phages as unique sensors of ecosystem features and environmental pressures. High-throughput sequencing approaches have begun to give us access to the diversity and range of phage populations in complex microbial community samples, and metagenomics is currently the primary tool with which we study phage populations. The study of phages by metagenomic sequencing, however, is fundamentally limited by viral diversity, which results in the vast majority of viral genomes and metagenome-annotated genomes lacking annotation. To harness bacteriophages for applications in human and environmental health and disease, we need new methods to organize and annotate viral sequence diversity. We recently demonstrated that methods that leverage self-supervised representation learning can supplement statistical sequence representations for remote viral protein homology detection in the ocean virome and propose that consideration of the functional content of viral sequences allows for the identification of similarity in otherwise sequence-diverse viruses and viral-like elements for biological discovery. In this review, we describe the potential and pitfalls of large language models for viral annotation. We describe the need for new approaches to annotate viral sequences in metagenomes, the fundamentals of what protein language models are and how one can use them for sequence annotation, the strengths and weaknesses of these models, and future directions toward developing better models for viral annotation more broadly.

Reconstructing SARS-CoV-2 lineages from mixed wastewater sequencing data

Wastewater surveillance of SARS-CoV-2 has emerged as a critical tool for tracking the spread of COVID-19. In addition to estimating the relative case numbers using quantitative PCR, SARS-CoV-2 genomic RNA can be extracted from wastewater and sequenced. There are many existing techniques for using the sequenced RNA to determine the relative abundance of known lineages in a sample. However, it is very challenging to predict novel lineages from wastewater data due to its mixed composition and unreliable genomic coverage. In this work, we present a novel technique based on non-negative matrix factorization which is able to reconstruct lineage definitions by analyzing data from across different samples. We test the method both on synthetic and real wastewater sequencing data. We show that the technique is able to determine major lineages such as Omicron and Delta as well as sub-lineages such as BA.5.2.1. We provide a method for determining emerging lineages in wastewater without the need for genomic data from clinical samples. This could be used for routine monitoring of SARS-CoV-2 as well as other emerging viral pathogens in wastewater. Additionally, it may be used to determine more full-genome sequences for viruses with fewer available genomes.

Decoding the DNA and RNA viromes of a tropical urban lagoon

Human and livestock sewage is one of the major causes of excess nutrients, leading to the eutrophication of aquatic ecosystems and potentially to the emergence or spread of pathogenic viruses. This study aimed to investigate the composition and diversity of aquatic viromes in a highly anthropized lagoon, to identify the presence of pathogenic taxa and to explore their use as possible viral indicators of faecal contamination. For this, water and sediment samples were collected in the Ebrié Lagoon (Ivory Coast) at seven stations with contrasting levels of eutrophication. The DNA viromes of the planktonic and the benthic compartments were highly divergent, but were not influenced by the level of eutrophication. Conversely, the RNA viromes in the water column were comparable to those found in sediment, but showed significant differences between the stations. We detected the presence of viral DNA and RNA sequences we had assigned as indicators of faecal contamination (smacovirus, pecovirus and pepper mild mottle virus) as well as human pathogens (human cyclovirus, coxsackie B virus and picobirnavirus), which were all enriched in the most eutrophicated sites. These findings suggest that the examination of viromes represents a promising tool for assessing the state of human-induced contamination of aquatic ecosystems.

Abundant dsRNA picobirnaviruses show little geographic or host association in terrestrial systems

Picobirnaviruses are double-stranded RNA viruses known from a wide range of host species and locations but with unknown pathogenicity and host relationships. Here, we examined the diversity of picobirnaviruses from cattle and gorillas within and around Bwindi Impenetrable Forest National Park (BIFNP), Uganda, where wild and domesticated animals and humans live in relatively close contact. We use metagenomic sequencing with bioinformatic analyses to examine genetic diversity. We compared our findings to global Picobirnavirus diversity using clustering-based analyses. Picobirnavirus diversity at Bwindi was high, with 14 near-complete RdRp and 15 capsid protein sequences, and 497 new partial viral sequences recovered from 44 gorilla samples and 664 from 16 cattle samples. Sequences were distributed throughout a phylogenetic tree of globally derived picobirnaviruses. The relationship with Picobirnavirus diversity and host taxonomy follows a similar pattern to the global dataset, generally lacking pattern with either host or geography.

Mapping human pathogens in wastewater using a metatranscriptomic approach

The monitoring of cities' wastewaters for the detection of potentially pathogenic viruses and bacteria has been considered a priority during the COVID-19 pandemic to monitor public health in urban environments. The methodological approaches frequently used for this purpose include deoxyribonucleic acid (DNA)/Ribonucleic acid (RNA) isolation followed by quantitative polymerase chain reaction (qPCR) and reverse transcription (RT)‒qPCR targeting pathogenic genes. More recently, the application of metatranscriptomic has opened opportunities to develop broad pathogenic monitoring workflows covering the entire pathogenic community within the sample. Nevertheless, the high amount of data generated in the process requires an appropriate analysis to detect the pathogenic community from the entire dataset. Here, an implementation of a bioinformatic workflow was developed to produce a map of the detected pathogenic bacteria and viruses in wastewater samples by analysing metatranscriptomic data. The main objectives of this work was the development of a computational methodology that can accurately detect both human pathogenic virus and bacteria in wastewater samples. This workflow can be easily reproducible with open-source software and uses efficient computational resources. The results showed that the used algorithms can predict potential human pathogens presence in the tested samples and that active forms of both bacteria and virus can be identified. By comparing the computational method implemented in this study to other state-of-the-art workflows, the implementation analysis was faster, while providing higher accuracy and sensitivity. Considering these results, the processes and methods to monitor wastewater for potential human pathogens can become faster and more accurate. The proposed workflow is available at https://github.com/waterpt/watermonitor and can be implemented in currently wastewater monitoring programs to ascertain the presence of potential human pathogenic species.

Picobirnaviruses in animals: a review

Picobirnaviruses (PBVs) are small non enveloped viruses with bi-segmented ds RNA. They have been observed in a wide variety of vertebrates, including mammals and birds with or without diarrhoea, as well as in sewage samples since its discovery (1988). The source of the viruses is uncertain. True hosts of PBVs and their role as primary pathogens or secondary opportunistic agents or innocuous viruses in the gut remains alien. The mechanisms by which they play a role in pathogenicity are still unclear based on the fact that they can be found in both symptomatic and asymptomatic cases. There is a need to determine their tropism since they have not only been associated with viral gastroenteritis but also been reported in the respiratory tracts of pigs. As zoonotic agents with diverse hosts, the importance of epidemiological and surveillance studies cannot be overstated. The segmented genome of PBV might pose a serious public health issue because of the possibility of continuous genetic reassortment. Aware of the growing attention being given to emerging RNA viruses, we reviewed the current knowledge on PBVs and described the current status of PBVs in animals.

Longitudinal metatranscriptomic sequencing of Southern California wastewater representing 16 million people from August 2020-21 reveals widespread transcription of antibiotic resistance genes

Municipal wastewater provides a representative sample of human fecal waste across a catchment area and contains a wide diversity of microbes. Sequencing wastewater samples provides information about human-associated and medically important microbial populations, and may be useful to assay disease prevalence and antimicrobial resistance (AMR). Here, we present a study in which we used untargeted metatranscriptomic sequencing on RNA extracted from 275 sewage influent samples obtained from eight wastewater treatment plants (WTPs) representing approximately 16 million people in Southern California between August 2020 - August 2021. We characterized bacterial and viral transcripts, assessed metabolic pathway activity, and identified over 2,000 AMR genes/variants across all samples. Because we did not deplete ribosomal RNA, we have a unique window into AMR carried as ribosomal mutants. We show that AMR diversity varied between WTPs (as measured through PERMANOVA, P < 0.001) and that the relative abundance of many individual AMR genes/variants increased over time (as measured with MaAsLin2, P_adj < 0.05). Similarly, we detected transcripts mapping to human pathogenic bacteria and viruses suggesting RNA sequencing is a powerful tool for wastewater-based epidemiology and that there are geographical signatures to microbial transcription. We captured the transcription of gene pathways common to bacterial cell processes, including central carbon metabolism, nucleotide synthesis/salvage, and amino acid biosynthesis. We also posit that due to the ubiquity of many viruses and bacteria in wastewater, new biological targets for microbial water quality assessment can be developed. To the best of our knowledge, our study provides the most complete longitudinal metatranscriptomic analysis of a large population's wastewater to date and demonstrates our ability to monitor the presence and activity of microbes in complex samples. By sequencing RNA, we can track the relative abundance of expressed AMR genes/variants and metabolic pathways, increasing our understanding of AMR activity across large human populations and sewer sheds.

A systematic review of enteric pathogens and antibiotic resistance genes in outdoor urban aerosols

Aerosol transport of enteric microbiota including fecal pathogens and antimicrobial resistance genes (ARGs) has been documented in a range of settings but remains poorly understood outside indoor environments. We conducted a systematic review of the peer-reviewed literature to summarize evidence on specific enteric microbiota including enteric pathogens and ARGs that have been measured in aerosol samples in urban settings where the risks of outdoor exposure and antibiotic resistance (AR) spread may be highest. Following PRISMA guidelines, we conducted a key word search for articles published within the years 1990-2020 using relevant data sources. Two authors independently conducted the keyword searches of databases and conducted primary and secondary screenings before merging results. To be included, studies contained extractable data on enteric microbes and AR in outdoor aerosols regardless of source confirmation and reported on qualitative, quantitative, or viability data on enteric microbes or AR. Qualitative analyses and metric summaries revealed that enteric microbes and AR have been consistently reported in outdoor aerosols, generally via relative abundance measures, though gaps remain preventing full understanding of the role of the aeromicrobiological pathway in the fate and transport of enteric associated outdoor aerosols. We identified remaining gaps in the evidence base including a need for broad characterization of enteric pathogens in bioaerosols beyond bacterial genera, a need for greater sampling in locations of high enteric disease risk, and a need for quantitative estimation of microbial and nucleic acid densities that may be applied to fate and transport models and in quantitative microbial risk assessment.

Investigation of the Presence of DNA of Highly Pathogenic Human Papillomaviruses in Water Bodies of the Lake Baikal Natural Territory

Human papillomaviruses (HPVs) are extremely widespread throughout the world. There are more than 100 types of HPVs, of which at least 14 types represent high oncogenic risk viruses (World Health Organization, 2020). Numerous attempts were made to analyze various water sources in order to (i) reveal the presence of DNA of pathogenic human papillomaviruses in them and (ii) assess the potential risks of occurrence of epidemics caused by HPV. With time, the necessity to solve these important problems stimulated the formation of a new direction in the world medical and environmental investigations.This paper contains the investigation of the presence of DNA of highly dangerous types of human papillomaviruses (HPV6, HPV11, HPV16 and HPV18) in water bodies of the Baikal natural territory, in particular in the water reservoirs in and near the villages of Listvyanka, Bolshiye Koty, Kultuk and the cities of Baikalsk and Slyudyanka. In course of our work, the conditions good for the study of the biological material obtained from water samples by the PCR technique to reveal the presence of DNA of HPV6, HPV11, HPV16 and HPV18 papillomaviruses were chosen. PCR analysis was conducted with the aid of both the already well-known universal primers GP5 + /6 + and the primers developed by our team to be applied to the conservative domains of nucleotide sequences encoding the main capsid protein L1 of human papillomaviruses HPV6, HPV11 (these types of the virus contribute to the occurrence of anogenital condylomatosis and the development of respiratory papillomatosis) and HPV16, HPV16 (these types of virus contribute to the occurrence of cervical cancer).The analyzes conducted by our team have revealed the presence of DNA of the four types of HPVs (6, 11, 16 and 18) in the samples taken from various water sources of the Baikal natural territory.

Longitudinal metatranscriptomic sequencing of Southern California wastewater representing 16 million people from August 2020-21 reveals widespread transcription of antibiotic resistance genes

Municipal wastewater provides a representative sample of human fecal waste across a catchment area and contains a wide diversity of microbes. Sequencing wastewater samples provides information about human-associated and medically-important microbial populations, and may be useful to assay disease prevalence and antimicrobial resistance (AMR). Here, we present a study in which we used untargeted metatranscriptomic sequencing on RNA extracted from 275 sewage influent samples obtained from eight wastewater treatment plants (WTPs) representing approximately 16 million people in Southern California between August 2020 - August 2021. We characterized bacterial and viral transcripts, assessed metabolic pathway activity, and identified over 2,000 AMR genes/variants across all samples. Because we did not deplete ribosomal RNA, we have a unique window into AMR carried as ribosomal mutants. We show that AMR diversity varied between WTPs and that the relative abundance of many individual AMR genes/variants increased over time and may be connected to antibiotic use during the COVID-19 pandemic. Similarly, we detected transcripts mapping to human pathogenic bacteria and viruses suggesting RNA sequencing is a powerful tool for wastewater-based epidemiology and that there are geographical signatures to microbial transcription. We captured the transcription of gene pathways common to bacterial cell processes, including central carbon metabolism, nucleotide synthesis/salvage, and amino acid biosynthesis. We also posit that due to the ubiquity of many viruses and bacteria in wastewater, new biological targets for microbial water quality assessment can be developed. To the best of our knowledge, our study provides the most complete longitudinal metatranscriptomic analysis of a large population's wastewater to date and demonstrates our ability to monitor the presence and activity of microbes in complex samples. By sequencing RNA, we can track the relative abundance of expressed AMR genes/variants and metabolic pathways, increasing our understanding of AMR activity across large human populations and sewer sheds.

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.

Integrating Virus Monitoring Strategies for Safe Non-potable Water Reuse

Wastewater reclamation and reuse have the potential to supplement water supplies, offering resiliency in times of drought and helping meet increased water demands associated with population growth. Non-potable water reuse represents the largest potential reuse market. Yet economic constraints for new water reuse infrastructure and safety concerns due to microbial water quality, and especially viral pathogen exposure, limit widespread implementation of water reuse. Cost-effective, real-time methods to measure or indicate viral quality of recycled water would do much to instill greater confidence in the practice. This manuscript discusses advancements in monitoring and modeling of viral health risks in the context of water reuse. First, we describe the current wastewater reclamation processes and treatment technologies with an emphasis on virus removal. Second, we review technologies for the measurement of viruses, both culture- and molecular-based, along with their advantages and disadvantages. We introduce promising viral surrogates and specific pathogenic viruses that can serve as indicators of viral risk for water reuse. We suggest metagenomic analyses for viral screening and flow cytometry for quantification of virus-like particles as new approaches to complement more traditional methods. Third, we describe modeling to assess health risks through quantitative microbial risk assessments (QMRAs), the most common strategy to couple data on virus concentrations with human exposure scenarios. We then explore the potential of artificial neural networks (ANNs) to incorporate suites of data from wastewater treatment processes, water quality parameters, and viral surrogates. We recommend ANNs as a means to utilize existing water quality data, alongside new complementary measures of viral quality, to achieve cost-effective strategies to assess risks associated with infectious human viruses in recycled water. Given the review, we conclude that technologies are ready for identifying and implementing viral surrogates for health risk reduction in the next decade. Incorporating modeling with monitoring data would likely result in more robust assessment of water reuse risk.

Genetic diversity, frequency and concurrent infections of picobirnaviruses in diarrhoeic calves in Turkey

Calf diarrhoea is one of the major problems in cattle farming with high morbidity and mortality in herds. Two enteric viruses, bovine rotavirus (BRV) and bovine coronavirus (BCoV), are the leading cause of gastroenteritis in young calves, whereas picobirnaviruses (PBVs) are often associated with diarrhoea. In the present study, the faecal specimens of 127 diarrhoeic bovines (less than 1-month-old) were employed to investigate the infection frequencies of these three pathogens. Results indicated that frequencies of BRV and BCoV in diarrhoeic calves were 38.58% and 29.92%, respectively. The 7.08% of bovine calf samples (9 out of 127) were found to be positive for PBV genogroup I. Sequence analysis further revealed the high genetic heterogeneity within representative PBV sequences. Additionally, both PBV-BCoV (n = 2) and BCoV-BRV-PBV (n = 1) co-infections were detected in bovine calves for the first time. Consequently, our findings pointed out the highly divergent nature of PBVs without regard to exact host or territory and the occasional co-existence with other enteric agents.

Comparative analysis of rapid concentration methods for the recovery of SARS-CoV-2 and quantification of human enteric viruses and a sewage-associated marker gene in untreated wastewater

To support public-health-related disease surveillance and monitoring, it is crucial to concentrate both enveloped and non-enveloped viruses from domestic wastewater. To date, most concentration methods were developed for non-enveloped viruses, and limited studies have directly compared the recovery efficiency of both types of viruses. In this study, the effectiveness of two different concentration methods (Concentrating pipette (CP) method and an adsorption-extraction (AE) method amended with MgCl₂) were evaluated for untreated wastewater matrices using three different viruses (SARS-CoV-2 (seeded), human adenovirus 40/41 (HAdV 40/41), and enterovirus (EV)) and a wastewater-associated bacterial marker gene targeting Lachnospiraceae (Lachno3). For SARS-CoV-2, the estimated mean recovery efficiencies were significantly greater by as much as 5.46 times, using the CP method than the AE method amended with MgCl₂. SARS-CoV-2 RNA recovery was greater for samples with higher titer seeds regardless of the method, and the estimated mean recovery efficiencies using the CP method were 25.1 ± 11% across ten WWTPs when wastewater samples were seeded with 5 × 10⁴ gene copies (GC) of SARS-CoV-2. Meanwhile, the AE method yielded significantly greater concentrations of indigenous HAdV 40/41 and Lachno3 from wastewater compared to the CP method. Finally, no significant differences in indigenous EV concentrations were identified in comparing the AE and CP methods. These data indicate that the most effective concentration method varies by microbial analyte and that the priorities of the surveillance or monitoring program should be considered when choosing the concentration method.

RNA Viromics of Southern California Wastewater and Detection of SARS-CoV-2 Single-Nucleotide Variants

Municipal wastewater provides an integrated sample of a diversity of human-associated microbes across a sewershed, including viruses. Wastewater-based epidemiology (WBE) is a promising strategy to detect pathogens and may serve as an early warning system for disease outbreaks. Notably, WBE has garnered substantial interest during the coronavirus disease 2019 (COVID-19) pandemic to track disease burden through analyses of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA. Throughout the COVID-19 outbreak, tracking SARS-CoV-2 in wastewater has been an important tool for understanding the spread of the virus. Unlike traditional sequencing of SARS-CoV-2 isolated from clinical samples, which adds testing burden to the health care system, in this study, metatranscriptomics was used to sequence virus directly from wastewater. Here, we present a study in which we explored RNA viral diversity through sequencing 94 wastewater influent samples across seven wastewater treatment plants (WTPs), collected from August 2020 to January 2021, representing approximately 16 million people in Southern California. Enriched viral libraries identified a wide diversity of RNA viruses that differed between WTPs and over time, with detected viruses including coronaviruses, influenza A, and noroviruses. Furthermore, single-nucleotide variants (SNVs) of SARS-CoV-2 were identified in wastewater, and we measured proportions of overall virus and SNVs across several months. We detected several SNVs that are markers for clinically important SARS-CoV-2 variants along with SNVs of unknown function, prevalence, or epidemiological consequence. Our study shows the potential of WBE to detect viruses in wastewater and to track the diversity and spread of viral variants in urban and suburban locations, which may aid public health efforts to monitor disease outbreaks. IMPORTANCE Wastewater-based epidemiology (WBE) can detect pathogens across sewersheds, which represents the collective waste of human populations. As there is a wide diversity of RNA viruses in wastewater, monitoring the presence of these viruses is useful for public health, industry, and ecological studies. Specific to public health, WBE has proven valuable during the coronavirus disease 2019 (COVID-19) pandemic to track the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) without adding burden to health care systems. In this study, we used metatranscriptomics and reverse transcription-droplet digital PCR (RT-ddPCR) to assay RNA viruses across Southern California wastewater from August 2020 to January 2021, representing approximately 16 million people from Los Angeles, Orange, and San Diego counties. We found that SARS-CoV-2 quantification in wastewater correlates well with county-wide COVID-19 case data, and that we can detect SARS-CoV-2 single-nucleotide variants through sequencing. Likewise, wastewater treatment plants (WTPs) harbored different viromes, and we detected other human pathogens, such as noroviruses and adenoviruses, furthering our understanding of wastewater viral ecology.

Comparison of faecal indicator and viral pathogen light and dark disinfection mechanisms in wastewater treatment pond mesocosms

This study compared light and dark disinfection of faecal bacteria/viral indicator organisms (E. coli and MS2 (fRNA) bacteriophage) and human viruses (Echovirus and Norovirus) in Wastewater Treatment Pond (WTP) mesocosms. Stirred pond mesocosms were operated in either outdoor sunlight-exposed or laboratory dark conditions in two experiments during the austral summer. To investigate wavelength-dependence of sunlight disinfection, three optical filters were used: (1) polyethylene film (light control: transmitting all solar UV and visible wavelengths), (2) acrylic (removing most UVB <315 nm), and (3) polycarbonate (removing both UVB and UVA <400 nm). To assess different dark disinfection processes WTP effluent was treated before spiking with target microbes, by (a) 0.22 μm filtration to remove all but colloidal particles, (b) 0.22 μm filtration followed by heat treatment to destroy enzymes, and (c) addition of Cytochalasin B to supress protozoan grazing. Microbiological stocks containing E. coli, MS2 phage, Echovirus, and Norovirus were spiked into each mesocosm 10 min before the experiments commenced. The light control exposed to all sunlight wavelengths achieved >5-log E. coli and MS2 phage removal (from ~1.0 × 10⁶ to <1 PFU/mL) within 3 h compared with up to 6 h in UV-filtered mesocosms. This result confirms that UVB contributes to inactivation of E. coli and viruses by direct sunlight inactivation. However, the very high attenuation with depth of UVB in WTP water (99% removal in the top 8 cm) suggests that UVB disinfection may be less important than other removal processes averaged over time and full-scale pond depth. Dark removal was appreciably slower than sunlight-mediated inactivation. The dark control typically achieved higher removal of E. coli and viruses than the 0.22 μm filtered (dark) mesocosms. This result suggests that adsorption of E. coli and viruses to WTP particles (e.g., algae and bacteria bio-flocs) is an important mechanism of dark disinfection, while bacteria and virus characteristics (e.g. surface charge) and environmental conditions can influence dark disinfection processes.

SARS-CoV-2 in hospital wastewater during outbreak of COVID-19: A review on detection, survival and disinfection technologies

Currently, the apparition of new SARS-CoV, known as SARS-CoV-2, affected more than 34 million people and causing high death rates worldwide. Recently, several studies reported SARS-CoV-2 ribonucleic acid (RNA) in hospital wastewater. SARS-CoV-2 can be transmitted between humans via respiratory droplets, close contact and fomites. Fecal-oral transmission is considered also as a potential route of transmission since several scientists confirmed the presence of SARS-CoV-2 RNA in feces of infected patients, therefore its transmission via feces in aquatic environment, particularly hospital wastewater. Hospitals are one of the important classes of polluting sectors around the world. It was identified that hospital wastewater contains hazardous elements and a wide variety of microbial pathogens and viruses. Therefore, this may potentially pose a significant risk of public health and environment infection. This study reported an introduction about the Physical-chemical and microbiological characterization of hospital wastewater, which can be a route to identify potential technology to reduce the impact of hospital contaminants before evacuation. The presence of SARS-CoV-2 in aqueous environment was reviewed. The knowledge of the detection and survival of SARS-CoV-2 in wastewater and hospital wastewater were described to understand the different routes of SARS-CoV-2 transmission, which is also useful to avoid the outbreak of CoV-19. In addition, disinfection technologies used commonly for deactivation of SARS-CoV-2 were highlighted. It was revealed that, chlorine-containing disinfectants are the most commonly used disinfectants in this field of research. Meanwhile, other efficient technologies must be developed and improved to avoid another wave of the pandemic of COVID-19 infections.

High Prevalence of Genogroup I and Genogroup II Picobirnaviruses in Dromedary Camels

Picobirnaviruses (PBVs) are small non-enveloped bisegmented double-stranded RNA viruses found in humans, mammals, and birds. Increasing molecular epidemiology studies suggest a high sequence diversity of PBVs in numerous hosts and the environment. In this study, using 229 fecal samples from dromedary camels in Dubai, 52.8% were positive for PBVs, of which 77.7% and 41.3% were positive for genogroup I and II, respectively, and 19.0% were positive for both genotypes. Phylogenetic analysis showed high diversity among the sequences of genogroup I and II dromedary PBVs. Marked nucleotide polymorphisms were observed in 75.5% and 46.0% of genogroup I and II RNA-dependent RNA polymerase (RdRp) sequences, respectively, suggesting the co-existence of multiple strains in the same specimen. Both high genetic diversity and prevalence of genogroup I and II PBV in dromedaries were observed. In fact, the prevalence of genogroup II PBV in dromedaries is the highest among all animals to date. The complete/near-complete core genomes of five genogroup I and one genogroup II dromedary PBVs and partial segment 1 and 2 of both genotypes were also sequenced. The dromedary PBV genome organizations were similar to those of other animals. Genetic reassortment and mutation are both important in the ecology and evolution of PBVs.

Molecular Detection of Human Enteric Adenoviruses in Water Samples Collected from Lake Victoria Waters Along Homa Bay Town, Homa Bay County, Kenya

Lake Victoria is the primary source of water for millions of people in the Sub-Saharan Africa region. In recent years, population development around the lake has resulted in compromised sanitation standards resulting in increased faecal pollution of the lake. Consequently, this condition has increased the chances of waterborne enteric viruses, such as adenoviruses' circulation in the community. Adenoviruses can affect health in both humans and animals by causing a myriad of diseases including the gastrointestinal infections. The study aimed to detect contamination of the lake water with pathogenic human adenoviruses along Homa Bay town, Homa Bay County, Kenya. To examine the presence of adenoviral genome, we collected a total of 216 (monthly n = 36) water samples from six different locations marked by high levels of anthropogenic activities along the shoreline. Molecular amplification technique using the nested PCR procedure was used to detect the genomes from the water samples. Human adenoviruses were detected in 11 samples (5.09%). Statistical analyses indicated a significant correlation between adenovirus presence and the approximate distance from pit latrines and sewage treatment works at the area. The findings indicate that faecal contamination of the lake waters originated from the point sources. The findings also suggest a possibility of elevated levels of faecal pollution in different surface waters within the lake basin. The findings indicate that some of the enteric viruses circulating in the local community are human adenovirus type 40, and 41. The data may provide a basis for recognizing the need to prioritize environmental monitoring for enteric virus contamination on an on-going basis.

Inactivation and Elimination of SARS-CoV-2 in Biosamples Using Simple Fixatives and Ultrafiltration

The Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) causes Coronavirus disease-2019 (COVID-19), which is an ongoing pandemic that has significantly affected the health, economy, and socio-economic status of individuals worldwide. Laboratory research using in vitro, ex vivo and in vivo models has been accelerated to understand the pathogenesis of SARS-CoV-2 infection. However, such experimental research involving SARS-CoV-2 is restricted to biocontainment/safety level-3 (BSL-3) settings, due to the high pathogenicity of this virus. Since many of the downstream analyses of SARS-CoV-2-infected biological samples need to be conducted in a non-BSL3 setting, it is important to ensure that the samples are fully decontaminated and safe for subsequent analysis. Here, we report the effectiveness of standard procedures used to fix cells and tissues for pathological analysis, including 2% or 4% paraformaldehyde, 50%–70% ethanol, 10% neutral buffered formalin and ultrafiltration using membranes with a molecular weight cut-off (MWCO) ranging from 3 to 30 kDa, for inactivating or eliminating SARS-CoV-2. We validated these methods in experimental laboratory samples, such as viral inoculum in cell culture media, SARS-CoV-2 infected host cells and animal tissue lysates. We found that 15 minutes’ treatment of viral inoculum (10⁵ plaque-forming units; PFU) or SARS-CoV-2 infected cells with paraformaldehyde or 70% ethanol resulted in complete inactivation of the virus. The treatment of infected hamster lung tissues with 10% neutral buffered formalin also fully inactivated the virus. However, only 3 kDa ultracentrifuge filter was effective in eliminating the virus to an undetectable limit in the filtrate. Our validated methods are useful for decontaminating biological samples to reduce infection risk and safe handling in BSL2 facilities.

Occurrence of Antibiotics, Antibiotic Resistance Genes and Viral Genomes in Wastewater Effluents and Their Treatment by a Pilot Scale Nanofiltration Unit

Broad-spectrum fluoroquinolone antibiotics (ciprofloxacin and levofloxacin), carbapenem and fluoroquinolone resistance genes, as well as viral genomes, were detected in grab samples of wastewater effluents. Passive samplers, which are simpler and easier to use and provide information about the concentrations and combination of contaminants present in a certain fluid matrix over time, proved to be extremely promising devices to monitor the presence of the target antibiotics in wastewater effluents. Nanofiltration was tested with a pilot-scale unit installed at a domestic wastewater treatment facility, using a Desal 5DK membrane operated at a constant transmembrane pressure of 6 bar and 70% recovery rate. In a 24 h experimental assay, the variation of the membrane permeance was low (6.3%). High rejections of the target contaminants from the wastewater effluent were obtained by the pilot-scale treatment. Hence, nanofiltration using the Desal 5DK membrane is considered to be a promising treatment to cope with chemical and biological contaminants present in wastewater effluents.

Viruses in wastewater: occurrence, abundance and detection methods

This paper presents an updated and comprehensive review on the different methods used for detection and quantification of viruses in wastewater treatment systems. The analysis of viability of viruses in wastewater and sludge is another thrust of this review. Recent studies have mostly focused on determining the abundance and diversity of viruses in wastewater influents, in samples from primary, secondary, and tertiary treatment stages, and in final effluents. A few studies have also examined the occurrence and diversity of viruses in raw and digested sludge samples. Recent efforts to improve efficiency of virus detection and quantification methods in the complex wastewater and sludge matrices are highlighted in this review. A summary and a detailed comparison of the pre-treatment methods that have been utilized for wastewater and sludge samples are also presented. The role of metagenomics or sequencing analysis in monitoring wastewater systems to predict disease outbreaks, to conduct public health surveillance, to assess the efficiency of existing treatment systems in virus removal, and to re-evaluate current regulations regarding pathogenic viruses in wastewater is discussed in this paper. Challenges and future perspectives in the detection of viruses, including emerging and newly emerged viruses such as the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), in wastewater systems are discussed in this review.

Picobirnaviruses: prevalence, genetic diversity, detection methods

This article presents a general overview of the prevalence, genetic diversity and detection methods of picobirnaviruses (PBVs), which are small, non-enveloped icosahedral viruses with a segmented double-stranded RNA genome consisting of two segments taxonomically related to the genus Picobirnavirus of the family Picobirnaviridae. This review of scientific papers published in 1988-2019 provides data on the PBV distribution in the nature and a broad host range. PBV infection is characterized as opportunistic, the lack of understanding of the etiological role of PBVs in diarrhea is emphasized, since these viruses are detected both in symptomatic and asymptomatic cases. The concept of PBV infection as a chronic disease caused by a long-lasting persistence of the virus in the host is considered. Such factors as stress syndrome, physiological conditions, immune status and host age at the time of primary PBV infection influence the virus detection rate in humans and animals. The possible zoonotic nature of human PBV infection is noted due to the capacity for interspecies PBV transmission acquired during evolution as a result of the reassortment of the genome segments of different viruses infecting the same host. Data providing evidence that PBVs belong to eukaryotes and a challenging hypothesis stating that PBVs are bacterial viruses are presented. The need to intensify work on PBV detection because of their wide distribution, despite the complexity due to the lack of the cultivation system, is emphasized. Two strategies of RT-PCR as main PBV detection methods are considered. The genomes of individual representatives of the genus isolated from different hosts are characterized. Emphasis is placed on the feasibility of developing primers with broader specificity for expanding the range of identifiable representatives of the genus PBV due to a huge variety of their genotypes. The importance of effective monitoring of PBV prevalence for studying the zoonotic and anthroponotic potential using metagenomic analysis is highlighted, and so is the possibility of using PBV as a marker for environmental monitoring.

Comparison of virus concentration methods for the RT-qPCR-based recovery of murine hepatitis virus, a surrogate for SARS-CoV-2 from untreated wastewater

There is currently a clear benefit for many countries to utilize wastewater-based epidemiology (WBE) as part of ongoing measures to manage the coronavirus disease 2019 (COVID-19) global pandemic. Since most wastewater virus concentration methods were developed and validated for nonenveloped viruses, it is imperative to determine the efficiency of the most commonly used methods for the enveloped severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Municipal wastewater seeded with a human coronavirus (CoV) surrogate, murine hepatitis virus (MHV), was used to test the efficiency of seven wastewater virus concentration methods: (A-C) adsorption-extraction with three different pre-treatment options, (D-E) centrifugal filter device methods with two different devices, (F) polyethylene glycol (PEG 8000) precipitation, and (G) ultracentrifugation. MHV was quantified by reverse-transcription quantitative polymerase chain reaction and the recovery efficiency was calculated for each method. The mean MHV recoveries ranged from 26.7 to 65.7%. The most efficient methods were adsorption-extraction methods with MgCl2 pre-treatment (Method C), and without pre-treatment (Method B). The third most efficient method used the Amicon® Ultra-15 centrifugal filter device (Method D) and its recovery efficiency was not statistically different from the most efficient methods. The methods with the worst recovery efficiency included the adsorption-extraction method with acidification (A), followed by PEG precipitation (F). Our results suggest that absorption-extraction methods with minimal or without pre-treatment can provide suitably rapid, cost-effective and relatively straightforward recovery of enveloped viruses in wastewater. The MHV is a promising process control for SARS-CoV-2 surveillance and can be used as a quality control measure to support community-level epidemic mitigation and risk assessment.

Metagenomic Insights into the Sewage RNA Virosphere of a Large City

Sewage-associated viruses can cause several human and animal diseases, such as gastroenteritis, hepatitis, and respiratory infections. Therefore, their detection in wastewater can reflect current infections within the source population. To date, no viral study has been performed using the sewage of any large South American city. In this study, we used viral metagenomics to obtain a single sample snapshot of the RNA virosphere in the wastewater from Santiago de Chile, the seventh largest city in the Americas. Despite the overrepresentation of dsRNA viruses, our results show that Santiago’s sewage RNA virosphere was composed mostly of unknown sequences (88%), while known viral sequences were dominated by viruses that infect bacteria (60%), invertebrates (37%) and humans (2.4%). Interestingly, we discovered three novel genogroups within the Picobirnaviridae family that can fill major gaps in this taxa’s evolutionary history. We also demonstrated the dominance of emerging Rotavirus genotypes, such as G8 and G6, that have displaced other classical genotypes, which is consistent with recent clinical reports. This study supports the usefulness of sewage viral metagenomics for public health surveillance. Moreover, it demonstrates the need to monitor the viral component during the wastewater treatment and recycling process, where this virome can constitute a reservoir of human pathogens.

Peracetic acid (PAA) and low-pressure ultraviolet (LP-UV) inactivation of Coxsackievirus B3 (CVB3) in municipal wastewater individually and concurrently

Domestic wastewater (WW) contains a large number of pathogenic viruses that are not significantly reduced in most WW treatment processes and are found in high numbers in the effluent of conventionally disinfected WW. In this study, secondary WW effluent bench-scale disinfection efficacy experiments with two different peracetic acid (PAA) formulations (15 and 22% peracetic acid) and low-pressure ultraviolet irradiation (LP-UV) were carried out using Coxsackievirus B3 (CVB3) as a clinically relevant surrogate for enteric viruses and Escherichia coli (E. coli) as the disinfection efficacy control. Efficacy experiments were done in a test matrix of medium-pressure UV (MP-UV) decontaminated secondary WW effluent under representative PAA doses and LP-UV fluences used at wastewater treatment plants (WWTP). Membrane filtration technique was used to determine Log₁₀ CFU reductions of E. coli and a tissue culture infectious dose 50% assay (TCID50) for Log₁₀ TCID50 reduction of CVB3. The CVB3 proved to be quite resistant to PAA with ≤1 Log₁₀ TCID50 reduction to concentrations ≤50 mg/L at a contact time of 15 min, and highly susceptible to LP-UV at 20 mJ/cm². Concurrent use of both formulations of 3 mg/L PAA with 20 mJ/cm² LP-UV achieved ∼4 Log₁₀ TCID50 reduction. The E. coli results showed ˃5 Log₁₀ CFU reductions at a contact time of 15 min with both 3 mg/L PAA formulations, 20 mJ/cm² LP-UV treatment alone, and combined with both 1.5 mg/L PAA formulations. The E. coli efficacy data were consistent with that reported in the literature and showed to be comparable to conventional chlorine disinfection. The CVB3 efficacy data has shown that PAA alone may not be suitable for the reduction of enteric viruses in secondary wastewater effluent, but this is also the case for chlorine-based disinfectants. The results from this study showed that the use of PAA with LP-UV at reasonable concentrations (1.5 mg/L) and fluence (20 mJ/cm²) can significantly reduce the PAA use and meet wastewater disinfection goals for both E. coli and CVs. However, the concurrent use of PAA with LP-UV did not lead to significant synergy in disinfection efficacy in wastewater.

Detection of SARS-CoV-2 RNA in commercial passenger aircraft and cruise ship wastewater: a surveillance tool for assessing the presence of COVID-19 infected travellers

BACKGROUND

Wastewater-based epidemiology (WBE) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can be an important source of information for coronavirus disease 2019 (COVID-19) management during and after the pandemic. Currently, governments and transportation industries around the world are developing strategies to minimize SARS-CoV-2 transmission associated with resuming activity. This study investigated the possible use of SARS-CoV-2 RNA wastewater surveillance from airline and cruise ship sanitation systems and its potential use as a COVID-19 public health management tool.

METHODS

Aircraft and cruise ship wastewater samples (n = 21) were tested for SARS-CoV-2 using two virus concentration methods, adsorption-extraction by electronegative membrane (n = 13) and ultrafiltration by Amicon (n = 8), and five assays using reverse-transcription quantitative polymerase chain reaction (RT-qPCR) and RT-droplet digital PCR (RT-ddPCR). Representative qPCR amplicons from positive samples were sequenced to confirm assay specificity.

RESULTS

SARS-CoV-2 RNA was detected in samples from both aircraft and cruise ship wastewater; however concentrations were near the assay limit of detection. The analysis of multiple replicate samples and use of multiple RT-qPCR and/or RT-ddPCR assays increased detection sensitivity and minimized false-negative results. Representative qPCR amplicons were confirmed for the correct PCR product by sequencing. However, differences in sensitivity were observed among molecular assays and concentration methods.

CONCLUSIONS

The study indicates that surveillance of wastewater from large transport vessels with their own sanitation systems has potential as a complementary data source to prioritize clinical testing and contact tracing among disembarking passengers. Importantly, sampling methods and molecular assays must be further optimized to maximize detection sensitivity. The potential for false negatives by both wastewater testing and clinical swab testing suggests that the two strategies could be employed together to maximize the probability of detecting SARS-CoV-2 infections amongst passengers.

Viral indicators for tracking domestic wastewater contamination in the aquatic environment

Waterborne enteric viruses are an emerging cause of disease outbreaks and represent a major threat to global public health. Enteric viruses may originate from human wastewater and can undergo rapid transport through aquatic environments with minimal decay. Surveillance and source apportionment of enteric viruses in environmental waters is therefore essential for accurate risk management. However, individual monitoring of the >100 enteric viral strains that have been identified as aquatic contaminants is unfeasible. Instead, viral indicators are often used for quantitative assessments of wastewater contamination, viral decay and transport in water. An ideal indicator for tracking wastewater contamination should be (i) easy to detect and quantify, (ii) source-specific, (iii) resistant to wastewater treatment processes, and (iv) persistent in the aquatic environment, with similar behaviour to viral pathogens. Here, we conducted a comprehensive review of 127 peer-reviewed publications, to critically evaluate the effectiveness of several viral indicators of wastewater pollution, including common enteric viruses (mastadenoviruses, polyomaviruses, and Aichi viruses), the pepper mild mottle virus (PMMoV), and gut-associated bacteriophages (Type II/III FRNA phages and phages infecting human Bacteroides species, including crAssphage). Our analysis suggests that overall, human mastadenoviruses have the greatest potential to indicate contamination by domestic wastewater due to their easy detection, culturability, and high prevalence in wastewater and in the polluted environment. Aichi virus, crAssphage and PMMoV are also widely detected in wastewater and in the environment, and may be used as molecular markers for human-derived contamination. We conclude that viral indicators are suitable for the long-term monitoring of viral contamination in freshwater and marine environments and that these should be implemented within monitoring programmes to provide a holistic assessment of microbiological water quality and wastewater-based epidemiology, improve current risk management strategies and protect global human health.

Occurrence of Enteric Viruses in Surface Water and the Relationship with Changes in Season and Physical Water Quality Dynamics

Environmental water quality issues have dominated global discourse and studies over the past five decades. Significant parameters of environmental water quality include changes in biological and physical parameters. Some of the biological parameters of significance include occurrence of enteric viruses. Enteric viruses can affect both human and animal's health by causing diseases such as gastrointestinal and respiratory infections. In this study, the relationship between the occurrence of enteric viruses with reference to adenoviruses and enteroviruses and the physical water quality characteristics was assessed from water samples collected from Lake Victoria (LV) in Kenya. In order to understand the dynamics of season driven enteric viruses' contamination of the lake waters, we additionally analysed seasonal behavior of the lake's catchment area in terms of rainfall effects. Physical quality parameters were measured on-site while viral analysis was carried out by molecular methods using the nested polymerase chain reaction (nPCR). From 216 samples that were analysed for viral contamination, enteric viral genomes were discovered in 18 (8.3%) of the samples. Out of half of the samples (108) collected during the rainy season, enteric viral genomes were detected in 9.26% (10) while 8 (7.41%) samples tested positive from the other half of the samples (108) collected during the dry season. There was, however, no significant correlation noted between the physical water quality characteristics and the enteric viruses' occurrence. Neither wet season nor dry season was significantly associated with the prevalence of the viruses. In Lake Victoria waters, most of the samples had an average of physical water quality parameters that were within the range accepted by the World Health Organization (WHO) for surface waters with exemption of turbidity which was above the recommended 5 NTU as recorded from some sampling sites. Continuous and long-term surveillance of the lake water to accurately monitor the contaminants and possible correlation between chemical, physical, and biological characteristics is recommended. This would be important in continuous understanding of the hydrological characteristics changes of the lake for proper management of its quality with reference to the WHO standards. A multiple varied-sampling approach in different geographical regions during different seasons is recommended to establish the geographical distribution and relatedness to seasonal distribution patterns of the viruses. The data generated from this study will be useful in providing a basis for assessment of seasonally driven fecal pollution load of the lake and enteric virus contamination for proper management of the sanitary situation around the lake.

Novel Picobirnaviruses in Respiratory and Alimentary Tracts of Cattle and Monkeys with Large Intra- and Inter-Host Diversity

Picobirnaviruses (PBVs) are mostly found in animal alimentary samples. In this study, among 576 respiratory specimens from 476 mammals and 100 chickens, genogroup I PBVs were detected in three cattle and three monkeys, and a genogroup II PBV-positive sample was collected from one cattle specimen. More than one PBV sequence type was observed in two and one genogroup I PBV-positive samples from cattle and monkeys, respectively. Twenty-four complete/near-complete segments 2 (nine from respiratory and 15 from alimentary samples) from the cattle and monkey genogroup I PBVs and one complete segment 2 from the cattle genogroup II PBV were sequenced. Similar to other studies, the cattle PBVs also showed a high diversity. In contrast, the monkey PBVs observed in this study were clustered into three distinct clades. Within each clade, all the sequences showed >99% amino acid identities. This unique phenomenon is probably due to the fact that monkeys in our locality reside in separated troops with minimal inter-troop contact.

Detection of potentially pathogenic enteric viruses in environmental samples from Kenya using the bag-mediated filtration system

Enteric virus environmental surveillance via a highly sensitive method is critical, as many enteric viruses have low infectious doses and can persist in the environment for extended periods. This study determined the potential of the novel bag-mediated filtration system (BMFS) to recover human enteric viruses and pepper mild mottle virus (PMMoV) from wastewater and wastewater-impacted surface waters, examined PMMoV use as a fecal contamination indicator in Kenya, and identified potential BMFS process controls. From April 2015 to April 2016, BMFS samples were collected from seven sites in Kenya (n = 59). Enteroviruses and PMMoV were detected in 100% of samples, and human adenovirus, human astrovirus, hepatitis A virus, norovirus GI, norovirus GII, sapovirus, and human rotavirus were detected in the majority of samples. The consistent detection of enteroviruses and PMMoV suggests that these viruses could be used as indicators in similarly fecally contaminated sites and BMFS process controls. As contamination of surface water sources remains a global issue, enteric virus environmental surveillance is necessary. This study demonstrates an effective way to sample large volumes of wastewater and wastewater-impacted surface waters for the detection of multiple enteric viruses simultaneously.

Coinfection of diarrheagenic bacterial and viral pathogens in piglets of Northeast region of India

AIM

This study aimed to study the prevalence of the coinfection of enteric bacterial and viral pathogens, namely Escherichia coli, Salmonella, Rotavirus, and Picobirnavirus from fecal samples of pre-weaned piglets in Northeast region of India.

MATERIALS AND METHODS

A total of 457 fresh fecal samples were collected from piglets under 9 weeks old during 2013-2015 from organized (n=225) and unorganized (n=232) farms of Manipur, Meghalaya, Mizoram, and Nagaland. Samples were collected from diarrheic (n =339) and non-diarrheic (n=118) piglets including local indigenous (n=130) and crossbreed (n=327) piglets in different seasons during the study period. The samples were processed for the isolation of E. coli and Salmonella and detection of their putative virulence genes by polymerase chain reaction (PCR). Samples were also processed for the detection of Rotavirus and Picobirnavirus by RNA-polyacrylamide agarose gel electrophoresis and reverse transcriptase-PCR (RT-PCR).

RESULTS

A total of 11 (2.40%) samples were found positive for two or more coinfecting enteric bacterial and viral pathogens. All the 11 positive fecal samples were recovered from diarrheic piglets. Salmonella Typhimurium (enterotoxin, stn gene) and Picobirnavirus genogroup 1 were found to be more frequent as coinfecting agents. Coinfection was recorded higher in unorganized (3.87%) compared to organized farm (0.88%). Again, higher detection was recorded in crossbreed (2.75%) than local indigenous piglets (1.53%). The occurrence of coinfection was found to be more common during summer (4.68%) followed by winter (2.27%) season.

CONCLUSION

The present study highlighted the significance of E. coli, Salmonella, Rotavirus, and Picobirnavirus as important diarrheagenic pathogens causing coinfection in piglets in Northeast region of India. Probably, this is the first systematic study of the coinfection of four important diarrheagenic bacterial and viral agents associated with piglet diarrhea in India.

Inactivation and Loss of Infectivity of Enterovirus 70 by Solar Irradiation

Enterovirus 70 (EV70) is an emerging viral pathogen that remains viable in final treated effluent. Solar irradiation is, therefore, explored as a low-cost natural disinfection strategy to mitigate potential concerns. EV70 was exposed to simulated sunlight for 24 h at a fluence rate of 28.67 J/cm2/h in three different water matrices, namely, phosphate-buffered saline (PBS), treated wastewater effluent, and chlorinated effluent. In the presence of sunlight, EV70 decreased in infectivity by 1.7 log, 1.0 log, and 1.3 log in PBS, effluent, and chlorinated effluent, respectively. Irradiated EV70 was further introduced to host cell lines and was unable to infect the cell lines. In contrast, EV70 in dark microcosms replicated to titers 13.5, 3.3, and 4.2 times the initial inoculum. The reduction in EV70 infectivity was accompanied by a reduction in viral binding capacity to Vero cells. In addition, genome sequencing analysis revealed five nonsynonymous nucleotide substitutions in irradiated viruses after 10 days of infection in Vero cells, resulting in amino acid substitutions: Lys14Glu in the VP4 protein, Ala201Val in VP2, Gly71Ser in VP3, Glu50Gln in VP1, and Ile47Leu in 3Cpro. Overall, solar irradiation resulted in EV70 inactivation and an inhibition of viral activity in all parameters studied.

UV inactivation of human infectious viruses at two full-scale wastewater treatment plants in Canada

Ultraviolet (UV) disinfection is widely used to inactivate microorganisms prior to release of treated municipal wastewater. However, limited data are available for in situ inactivation of infectious enteric viruses by UV treatment at full-scale. In this study, a total of 51 pre-UV and 50 post-UV samples were collected over a two-year period from two wastewater treatment plants (WWTPs) and analyzed for noroviruses, rotavirus, reovirus, sapovirus, astrovirus, enteroviruses, adenoviruses and JC virus. Both pre-UV and post-UV samples had relatively high concentrations of these viruses determined by qPCR. Infectious viruses were also observed in 98% of pre-UV samples and 76% of post-UV samples by cell culture, using either cytopathic effect (CPE) or integrated cell culture with qPCR (ICC-qPCR). Reovirus was the most common virus detected by ICC-qPCR, present in 92% of pre-UV and 48% of post-UV samples. Infectious enterovirus and adenovirus were detected by ICC-qPCR in 33% and 31% of pre-UV samples, 14% and 20% of post-UV samples, respectively. Mean log₁₀ reduction estimates for infectious reovirus was 1.2 and 1.8 log for the two WWTPs as assessed by ICC-qPCR, which was similar to the reduction of total infectious viruses (1.5 and 1.7 log) as assessed by CPE in cells culture. Overall, quantification of infectious reovirus appears to provide a useful index of enteric virus inactivation during wastewater treatment at full-scale. To our knowledge, this is the first comprehensive study to assess UV inactivation of human enteric viruses at full-scale in WWTPs using both molecular and cell culture techniques, providing important information for quantitative microbial risk assessment of UV inactivation of human viruses in municipal wastewater.

The Challenges of Analysing Highly Diverse Picobirnavirus Sequence Data

The reliable identification and classification of infectious diseases is critical for understanding their biology and controlling their impact. Recent advances in sequencing technology have allowed insight into the remarkable diversity of the virosphere, of which a large component remains undiscovered. For these emerging or undescribed viruses, the process of classifying unknown sequences is heavily reliant on existing nucleotide sequence information in public databases. However, due to the enormous diversity of viruses, and past focus on the most prevalent and impactful virus types, databases are often incomplete. Picobirnaviridae is a dsRNA virus family with broad host and geographic range, but with relatively little sequence information in public databases. The family contains one genus, Picobirnavirus, which may be associated with gastric illness in humans and animals. Little further information is available due in part to difficulties in identification. Here, we investigate diversity both within the genus Picobirnavirus and among other dsRNA virus types using a combined phylogenetic and functional (protein structure homology-modelling) approach. Our results show that diversity within picobirnavirus exceeds that seen between many other dsRNA genera. Furthermore, we find that commonly used practices employed to classify picobirnavirus, such as analysis of short fragments and trimming of sequences, can influence phylogenetic conclusions. The degree of phylogenetic and functional divergence among picobirnavirus sequences in our study suggests an enormous undiscovered diversity, which contributes to the undescribed “viral dark matter” component of metagenomic studies.

Molecular characterization of a novel picobirnavirus in a chicken

Picobirnaviruses (PBVs) are bisegmented viruses with a wide geographical and host species distribution. The number of novel PBV sequences has been increasing with the help of the viral metagenomics. A novel picobirnavirus strain, pbv/CHK/M3841/HUN/2011, was identified by viral metagenomics; the complete segment 1 (MH327933) and 2 (MH327934) sequences were obtained by RT-PCR from a cloacal sample of a diseased broiler breeder pullet in Hungary. Although the conserved nucleotide (e.g., ribosome binding site) and amino acid motifs (e.g., ExxRxNxxxE, S-domain of the viral capsid and motifs in the RNA-dependent RNA polymerase) were identifiable in the chicken picobirnavirus genome, the putative segment 1 showed low (< 30%) amino acid sequence identity to the corresponding proteins of marmot and dromedary PBVs, while segment 2 showed higher (< 70%) amino acid sequence identity to a wolf PBV protein sequence. This is the first full-genome picobirnavirus sequence from a broiler breeder chicken, but the pathogenicity of this virus is still questionable.

Persistence of Viruses by qPCR Downstream of Three Effluent-Dominated Rivers in the Western United States

This study was designed to determine the quantitative polymerase chain reaction (qPCR) signal persistence of viruses in three effluent-dominated streams. Samples were collected from the effluent outfall of three wastewater treatment plants in the Western United States and downstream at different locations. All samples were tested for the presence of pepper mild mottle virus (PMMoV), adenoviruses, norovirus GI and GII, Aichi virus, and enteroviruses using qPCR. PMMoV was detected most frequently in 54/57 (94.7%) samples, followed by adenoviruses which was detected in 21/57 (36.8%) samples. PMMoV was detected at all locations downstream and up to 32 km from the discharge point. This study demonstrated that the detection signal of PMMoV was able to persist in wastewater discharges to a greater degree than human enteric viruses in effluent-dominated rivers.

Geospatial distribution of viromes in tropical freshwater ecosystems

This study seeks to understand the general distribution of virome abundance and diversity in tropical freshwater ecosystems in Singapore and the geospatial distribution of the virome under different landuse patterns. Correlations between diversity, environmental parameters and land use patterns were analyzed and significant correlations were highlighted. Overall, the majority (65.5%) of the annotated virome belonged to bacteriophages. The percentage of Caudovirales was higher in reservoirs whereas the percentages of Dicistroviridae, Microviridae and Circoviridae were higher in tributaries. Reservoirs showed a higher Shannon-index virome diversity compared to upstream tributaries. Land use (urbanized, agriculture and parkland areas) influenced the characteristics of the virome distribution pattern. Dicistroviridae and Microviridae were enriched in urbanized tributaries while Mimiviridae, Phycodnaviridae, Siphoviridae and Podoviridae were enriched in parkland reservoirs. Several sequences closely related to the emerging zoonotic virus, cyclovirus, and the human-related virus (human picobirnavirus), were also detected. In addition, the relative abundance of PMMoV (pepper mild mottle virus) sequences was significantly correlated with RT-qPCR measurements (0.588 < r < 0.879, p < 0.05). This study shows that spatial factors (e.g., reservoirs/tributaries, land use) are the main drivers of the viral community structure in tropical freshwater ecosystems.

Detection of novel RNA viruses from free-living gorillas, Republic of the Congo: genetic diversity of picobirnaviruses

Most of the emerging infectious diseases reported so far originated in wildlife. Therefore, virological surveillance of animals and particularly great apes is of great interest to establish the repertory of viruses associated with healthy hosts. This will further help to identify the emergence of new viruses and predict the possibility of interspecies transmission. In this study, we performed shotgun viral metagenomics on stool samples collected from seventeen free-living wild gorillas from the Republic of the Congo. The analysis revealed the presence of novel RNA viruses (picobirnaviruses, partitivirus, and Picornavirales (posa-like and dicistrovirus-like viruses)). Among these, picobirnavirus-related sequences were abundantly covered in the stools. Based on genetic variations both in capsid and RdRp proteins of picobirnaviruses, at least 96 variants were identified and most of them were novel. Among the 96, 22 variants had a nearly complete genome or segment. A comprehensive sequence analysis identified a potential new genogroup/genetic cluster and the presence of a short linear amino acid motif (ExxRxNxxxE) in a hypothetical protein. The sequence analysis of posa-like virus and dicistrovirus showed that these two viruses were novel members in the respective viral families. In conclusion, the identification of novel RNA viruses and their genetic diversity increases our knowledge about viruses that are associated with stools of wild gorillas and contributes to the initiatives in the search for potential emerging zoonotic viruses.

Metagenomics for the study of viruses in urban sewage as a tool for public health surveillance

The application of next-generation sequencing (NGS) techniques for the identification of viruses present in urban sewage has not been fully explored. This is partially due to a lack of reliable and sensitive protocols for studying viral diversity and to the highly complex analysis required for NGS data processing. One important step towards this goal is finding methods that can efficiently concentrate viruses from sewage samples. Here the application of a virus concentration method based on skimmed milk organic flocculation (SMF) using 10L of sewage collected in different seasons enabled the detection of many viruses. However, some viruses, such as human adenoviruses, could not always be detected using metagenomics, even when quantitative PCR (qPCR) assessments were positive. A targeted metagenomic assay for adenoviruses was conducted and 59.41% of the obtained reads were assigned to murine adenoviruses. However, up to 20 different human adenoviruses (HAdV) were detected by this targeted assay being the most abundant HAdV-41 (29.24%) and HAdV-51 (1.63%). To improve metagenomics' sensitivity, two different protocols for virus concentration were comparatively analysed: an ultracentrifugation protocol and a lower-volume SMF protocol. The sewage virome contained 41 viral families, including pathogenic viral species from families Caliciviridae, Adenoviridae, Astroviridae, Picornaviridae, Polyomaviridae, Papillomaviridae and Hepeviridae. The contribution of urine to sewage metavirome seems to be restricted to a few specific DNA viral families, including the polyomavirus and papillomavirus species. In experimental infections with sewage in a rhesus macaque model, infective human hepatitis E and JC polyomavirus were identified. Urban raw sewage consists of the excreta of thousands of inhabitants; therefore, it is a representative sample for epidemiological surveillance purposes. The knowledge of the metavirome is of significance to public health, highlighting the presence of viral strains that are circulating within a population while acting as a complex matrix for viral discovery.

Iron oxide-mediated semiconductor photocatalysis vs. heterogeneous photo-Fenton treatment of viruses in wastewater. Impact of the oxide particle size

The photo-Fenton process is recognized as a promising technique towards microorganism disinfection in wastewater, but its efficiency is hampered at near-neutral pH operating values. In this work, we overcome these obstacles by using the heterogeneous photo-Fenton process as the default disinfecting technique, targeting MS2 coliphage in wastewater. The use of low concentrations of iron oxides in wastewater without H₂O₂ (wüstite, maghemite, magnetite) has demonstrated limited semiconductor-mediated MS2 inactivation. Changing the operational pH and the size of the oxide particles indicated that the isoelectric point of the iron oxides and the active surface area are crucial in the success of the process, and the possible underlying mechanisms are investigated. Furthermore, the addition of low amounts of Fe-oxides (1mgL^-1) and H₂O₂ in the system (1, 5 and 10mgL^-1) greatly enhanced the inactivation process, leading to heterogeneous photo-Fenton processes on the surface of the magnetically separable oxides used. Additionally, photo-dissolution of iron in the bulk, lead to homogeneous photo-Fenton, further aided by the complexation by the dissolved organic matter in the solution. Finally, we assess the impact of the presence of the bacterial host and the difference caused by the different iron sources (salts, oxides) and the Fe-oxide size (normal, nano-sized).

Diverse and highly recombinant anelloviruses associated with Weddell seals in Antarctica

The viruses circulating among Antarctic wildlife remain largely unknown. In an effort to identify viruses associated with Weddell seals (Leptonychotes weddellii) inhabiting the Ross Sea, vaginal and nasal swabs, and faecal samples were collected between November 2014 and February 2015. In addition, a Weddell seal kidney and South Polar skua (Stercorarius maccormicki) faeces were opportunistically sampled. Using high throughput sequencing, we identified and recovered 152 anellovirus genomes that share 63–70% genome-wide identities with other pinniped anelloviruses. Genome-wide pairwise comparisons coupled with phylogenetic analysis revealed two novel anellovirus species, tentatively named torque teno Leptonychotes weddellii virus (TTLwV) -1 and -2. TTLwV-1 (n = 133, genomes encompassing 40 genotypes) is highly recombinant, whereas TTLwV-2 (n = 19, genomes encompassing three genotypes) is relatively less recombinant. This study documents ubiquitous TTLwVs among Weddell seals in Antarctica with frequent co-infection by multiple genotypes, however, the role these anelloviruses play in seal health remains unknown.

Waterborne Viruses and F-Specific Coliphages in Mixed-Use Watersheds: Microbial Associations, Host Specificities, and Affinities with Environmental/Land Use Factors

From the years 2008 to 2014, a total of 1,155 water samples were collected (spring to fall) from 24 surface water sampling sites located in a mixed-used but predominantly agricultural (i.e., dairy livestock production) river basin in eastern Ontario, Canada. Water was analyzed for viable F-specific DNA (F-DNA) and F-specific RNA (F-RNA) (genogroup I [GI] to GIV) coliphage and a suite of molecularly detected viruses (norovirus [GI to GIV], torque teno virus [TTV], rotavirus, kobuvirus, adenovirus, astrovirus, hepatitis A, and hepatitis E). F-DNA and F-RNA coliphage were detected in 33 and 28% of the samples at maximum concentrations of 2,000 and 16,300 PFU · 100 ml^-1, respectively. Animal TTV, human TTV, kobuvirus, astrovirus, and norovirus GIII were the most prevalent viruses, found in 23, 20, 13, 12, and 11% of samples, respectively. Viable F-DNA coliphage was found to be a modest positive indicator of molecularly detected TTV. F-RNA coliphage, unlike F-DNA coliphage, was a modest positive predictor of norovirus and rotavirus. There were, however, a number of significant negative associations among F-specific coliphage and viruses. F-DNA coliphage densities of >142 PFU · 100 ml^-1 delineated conditions when ∼95% of water samples contained some type of virus. Kobuvirus was the virus most strongly related to detection of any other virus. Land use had some associations with virus/F-specific coliphage detection, but season and surface water flow were the variables that were most important for broadly delineating detection. Higher relative levels of detection of human viruses and human F-RNA coliphage were associated with higher relative degrees of upstream human land development in a catchment.

IMPORTANCE

This study is one of the first, to our knowledge, to evaluate relationships among F-specific coliphages and a large suite of enteric viruses in mixed-use but agriculturally dominated surface waters in Canada. This study suggested that relationships between viable F-specific coliphages and molecularly detected viruses do exist, but they are not always positive. Caution should be employed if viable F-specific coliphages are to be used as indicators of virus presence in surface waters. This study elucidates relative effects of agriculture, wildlife, and human activity on virus and F-specific coliphage detection. Seasonal and meteorological attributes play a strong role in the detection of most virus and F-specific coliphage targets.

Prevalence and molecular characterization of porcine Picobirnavirus in piglets of North East Region of India

Picobirnaviruses (PBVs) have been recognized as one of the important causal viral agents of gastroenteritis in several animal species especially in young immunocompromised hosts. In this study, we report the prevalence and molecular epidemiology of porcine PBVs from North Eastern Hilly region of India. A total of 457 fecal samples from piglets were collected from local (n = 130) and cross (n = 327) breed piglets in different seasons for 2 years. All the samples were subjected to RNA-PAGE and RT-PCR analysis for detection of PBVs. A total of 4.59 and 11.15% samples were recorded as positive for PBVs by RNA-PAGE and RT-PCR, respectively. Rate of detection was higher from diarrhoeic animals (13.56%) compared to non-diarrhoeic (4.23%) animals. Higher prevalence rate was observed from unorganized farms (14.22%) compared to organized farms (8.0%) with slightly higher detection from cross breed (11.62%) compared to local breed (10.0%). Maximum cases of piglet diarrhea associated with PBVs were detected during summer (16.4%) and winter (14.39%) seasons compared to autumn (4.80%) and spring (6.45%). All the samples were positive for PBV genogroup I only. Based upon the sequence analysis, the isolates were unique and placed in separate clad and were not closely associated with any other Indian isolates of PBVs so far. Two isolates were closely related with one Chinese isolate recovered from sewage water. This is the first systematic study of prevalence of PBVs associated with piglet diarrhea.

Quantitative PCR Detection and Characterisation of Human Adenovirus, Rotavirus and Hepatitis A Virus in Discharged Effluents of Two Wastewater Treatment Facilities in the Eastern Cape, South Africa

The occurrence of enteric viruses in reclaimed wastewater, their removal by efficient treatment processes and the public health hazards associated with their release into the environments are of great significance in environmental microbiology. In this study, TaqMan-based real-time polymerase chain reaction (qPCR) was used to assess the prevalence of human adenovirus (HAdV), rotavirus (RV) and hepatitis A virus (HAV) in the final effluents of two wastewater treatment plants in the Eastern Cape Province, South Africa, over a twelve-month sampling period. The correlation between the concentrations of viruses in the effluents samples and faecal coliform (FC) densities were assessed as to validate the use of FC as microbiological indicator in water quality assessment. HAdV was detected in 62.5 % (30/48) of the samples with concentrations ranging between 8.4 × 101 and 1.0 × 105 genome copies/L while HAV and RV were only detected at concentrations below the set detection limits. FCs densities ranged from 1 to 2.7 × 104 CFU/100 ml. Adenovirus species HAdV-B (serotype 2) and HAdV-F (serotype 41) were detected in 86.7 % (26/30) and 6.7 % (2/30) of the HAdV-positive samples, respectively. No consistent seasonal trend was observed in HAdV concentrations, however, increased concentrations of HAdV were generally observed in the winter months. Also, there was no correlation between the occurrence of HAdV and FC at both the treatment plants. The persistent occurrence of HAdV in the discharged treated effluents points to the potential public health risk through the release of HAdV into the receiving watersheds, and the possibility of their transmission to human population.

High Diversity of Genogroup I Picobirnaviruses in Mammals

In a molecular epidemiology study using 791 fecal samples collected from different terrestrial and marine mammals in Hong Kong, genogroup I picobirnaviruses (PBVs) were positive by RT-PCR targeting the partial RdRp gene in specimens from five cattle, six monkeys, 17 horses, nine pigs, one rabbit, one dog, and 12 California sea lions, with 11, 9, 23, 17, 1, 1, and 15 sequence types in the positive specimens from the corresponding animals, respectively. Phylogenetic analysis showed that the PBV sequences from each kind of animal were widely distributed in the whole tree with high diversity, sharing 47.4–89.0% nucleotide identities with other genogroup I PBV strains based on the partial RdRp gene. Nine complete segment 1 (viral loads 1.7 × 10⁴ to 5.9 × 10⁶/ml) and 15 segment 2 (viral loads 4.1 × 10³ to 1.3 × 10⁶/ml) of otarine PBVs from fecal samples serially collected from California sea lions were sequenced. In the two phylogenetic trees constructed using ORF2 and ORF3 of segment 1, the nine segment 1 sequences were clustered into four distinct clades (C1–C4). In the tree constructed using RdRp gene of segment 2, the 15 segment 2 sequences were clustered into nine distinct clades (R1–R9). In four sea lions, PBVs were detected in two different years, with the same segment 1 clade (C3) present in two consecutive years from one sea lion and different clades present in different years from three sea lions. A high diversity of PBVs was observed in a variety of terrestrial and marine mammals. Multiple sequence types with significant differences, representing multiple strains of PBV, were present in the majority of PBV-positive samples from different kinds of animals.

Rethinking the Significance of Reovirus in Water and Wastewater

The genus Orthoreovirus contains nonenveloped viruses with double-stranded gene segments encased in a double-layered icosahedral capsid shell. These features constitute major determinants of virion stability in the environment and virion resistance against physical and chemical agents. Reovirus (ReoV) is the general term most commonly used for all virus strains that infect humans and nonhuman animals. Several studies have demonstrated the frequent occurrence of ReoV in wastewaters and natural waters, including surface and ground waters from different geographical areas. Most of these studies have reported higher concentrations of ReoV than any other enteric virus analyzed. They are more commonly isolated in chlorine-disinfected wastewaters than other enteric viruses, and appear to survive longer in water. The ability of ReoV to form large aggregates, even with different types of enteric viruses (e.g., poliovirus) and their ability to undergo mechanisms of gene segment reassortment among different serotypes may also explain their greater stability. Different approaches have been applied for concentration of ReoV from water; however, the recovery efficiency of the filtration methods has not been fully evaluated. Recently, molecular methods for identification of ReoV strains and quantification of virus genome have been developed. Studies have shown that the overall detection sensitivity of ReoV RNA is enhanced through initial replication of infectious virions in cell culture. More studies are needed to specifically address unresolved issues about the fate and distribution of ReoV in the environment since this virus is not commonly included in virological investigations.

Tracking Human Adenovirus Inactivation by Gamma Radiation under Different Environmental Conditions

Adenovirus is the most prevalent enteric virus in waters worldwide due to its environmental stability, which leads to public health concerns. Mitigation strategies are therefore required. The aim of this study was to assess the inactivation of human adenovirus type 5 (HAdV-5) by gamma radiation in aqueous environments. Various substrates with different organic loads, including domestic wastewater, were inoculated with HAdV-5 either individually or in a viral pool (with murine norovirus type 1 [MNV-1]) and were irradiated in a Cobalt-60 irradiator at several gamma radiation doses (0.9 to 10.8 kGy). The infectivity of viral particles, before and after irradiation, was tested by plaque assay using A549 cells. D10 values (dose required to inactivate 90% of a population or the dose of irradiation needed to produce a 1 log10 reduction in the population) were estimated for each substrate based on virus infectivity inactivation exponential kinetics. The capability of two detection methods, nested PCR and enzyme-linked immunosorbent assay (ELISA), to track inactivated viral particles was also assessed. After irradiation at 3.5 kGy, a reduction of the HAdV-5 titer of 4 log PFU/ml on substrates with lower organic loads was obtained, but in highly organic matrixes, the virus titer reduction was only 1 log PFU/ml. The D10 values of HAdV-5 in high organic substrates were significantly higher than in water suspensions. The obtained results point out some discrepancies between nested PCR, ELISA, and plaque assay on the assessments of HAdV-5 inactivation. These results suggest that the inactivation of HAdV-5 by gamma radiation, in aqueous environments, is significantly affected by substrate composition. This study highlights the virucidal potential of gamma radiation that may be used as a disinfection treatment for sustainable water supplies.

IMPORTANCE

Human adenovirus (HAdV) is the most prevalent of the enteric viruses in environmental waters worldwide. The purposes of this study are to provide new insights on the inactivation of enteric virus by gamma irradiation and to introduce new concepts and reinforce the benefits and utility of radiation technologies as disinfection processes. This may be an effective tool to guarantee the reduction of viral pathogens and to contribute to public health and sustainable water supplies.