Gastroenteric Viruses Detection in a Drinking Water Distribution-to-Consumption System in a Low-Income Community in Rio de Janeiro

Metatranscriptomic data mining together with microfluidic card uncovered the potential pathogens and seasonal RNA viral ecology in a drinking water source

AIMS

Despite metatranscriptomics becoming an emerging tool for pathogen surveillance, very little is known about the feasibility of this approach for understanding the fate of human-derived pathogens in drinking water sources.

METHODS AND RESULTS

We conducted multiplexed microfluidic cards and metatranscriptomic sequencing of the drinking water source in a border city of North Korea in four seasons. Microfluidic card detected norovirus, hepatitis B virus (HBV), enterovirus, and Vibrio cholerae in the water. Phylogenetic analyses showed that environmental-derived sequences from norovirus GII.17, genotype C of HBV, and coxsackievirus A6 (CA6) were genetically related to the local clinical isolates. Meanwhile, metatranscriptomic assembly suggested that several bacterial pathogens, including Acinetobacter johnsonii and V. cholerae might be prevalent in the studied region. Metatranscriptomic analysis recovered 349 species-level groups with substantial viral diversity without detection of norovirus, HBV, and CA6. Seasonally distinct virus communities were also found. Specifically, 126, 73, 126, and 457 types of viruses were identified in spring, summer, autumn, and winter, respectively. The viromes were dominated by the Pisuviricota phylum, including members from Marnaviridae, Dicistroviridae, Luteoviridae, Potyviridae, Picornaviridae, Astroviridae, and Picobirnaviridae families. Further phylogenetic analyses of RNA (Ribonucleic Acid)-dependent RNA polymerase (RdRp) sequences showed a diverse set of picorna-like viruses associated with shellfish, of which several novel picorna-like viruses were also identified. Additionally, potential animal pathogens, including infectious bronchitis virus, Bat dicibavirus, Bat nodavirus, Bat picornavirus 2, infectious bursal disease virus, and Macrobrachium rosenbergii nodavirus were also identified.

CONCLUSIONS

Our data illustrate the divergence between microfluidic cards and metatranscriptomics, highlighting that the combination of both methods facilitates the source tracking of human viruses in challenging settings without sufficient clinical surveillance.

Occurrence of human pathogenic viruses in drinking water and in its sources: A review

Since many waterborne diseases are caused by human pathogenic viruses, virus monitoring of drinking water (DW) and DW sources is crucial for public health. Therefore, the aim of this review was to describe the occurrence of human pathogenic viruses in DW and DW sources; the occurrence of two viruses proposed as novel indicators of human faecal contamination (Pepper mild mottle virus and Tobacco mosaic virus) was also reported. This research was focused on articles that assessed viral occurrence using molecular methods in the surface water used for DW production (SW-D), groundwater used for DW production (GW-D), DW and bottled-DW (BW). A total of 1544 studies published in the last 10 years were analysed, and 79 were ultimately included. In considering the detection methods, filtration is the most common concentration technique, while quantitative polymerase chain reaction is the most common quantification technique. Regarding virus occurrence in SW-D, GW-D, and DW, high percentages of positive samples were reported for adenovirus, polyomavirus and Pepper mild mottle virus. Viral genomes were frequently detected in SW-D and rarely in GW-D, suggesting that GW-D may be a safe DW source. Viral genomes were also detected in DW, posing a possible threat to human health. The lowest percentages of positive samples were found in Europe, while the highest were found in Asia and South America. Only three articles assessed viral occurrence in BW. This review highlights the lack of method standardization and the need for legislation updates.

Investigation of Human and Animal Viruses in Water Matrices from a Rural Area in Southeastern Region of Brazil and Their Potential Use as Microbial Source-Tracking Markers

This study assessed the sources of contamination of water matrices in a rural area using detection of a host-specific virus (human adenovirus [HAdV], porcine adenovirus [PAdV] and bovine polyomaviruses [BoPyV]) as potential microbial source-tracking tool, and rotavirus A [RVA], given its epidemiological importance in Brazil. From July 2017 to June 2018, 92 samples were collected from eight points (P1-P8) of surface and raw waters in southeastern region of Brazil. Fifty-five (59.8%) were positive for HAdV, 41 (44.5%) for RVA, 10 (10.9%) for PAdV and four (4.3%) for BoPyV. HAdV and RVA were detected at all sites, and over the entire sampling period, PAdV was detected at a porcine breeding area and at Guarda River site, presenting high concentrations up to 2.6 × 10⁹ genome copies per liter [GC/L], and viral concentrations ranging from 9.6 × 10¹ to 7.1 × 10⁷, while BoPyV (1.5 × 10⁴ GC/L-9.2 × 10⁵ GC/L) was only detected in samples from the bovine breeding areas. The combination of human and animal virus circulation presents a potential impact in the environment due to raw sewage discharge from regional communities, as well as potential hazard to human and animal health.

Physicochemical, microbiological quality, and risk assessment of water consumed by a quilombola community in midwestern Brazil

The quality of the water consumed by a given community is related to its quality of life. In this sense, this study aimed to evaluate, from the perspective of health risk, the physical, chemical, and microbiological quality of drinking water, in a quilombola community, and the qualitative aspects intrinsic to its use and storage. For this, water samples, collected at the exits of the collective water supply system and from eight cisterns that store rainwater, used for human consumption, were analyzed. The samples were subjected to physical, chemical, and microbiological analysis, including adenovirus (HAdV) and enterovirus (EV). The probability of an individual acquiring infection through water consumption was determined by quantitative microbiological risk analysis using HAdV and Escherichia coli (EC) as reference pathogens. The results showed that the water in the deep tubular well had 270.8 mg/L of total hardness, leading to the rejection of its consumption by ingestion. Alternativity, the people in the community consume rainwater stored in cisterns. For this type of water, the presence of heterotrophic bacteria was found in 75%, total coliform was present in 100%, and Enterococci were detected in 25%. Furthermore, EC was present in 25%, EV in 50%, and HAdV in 100% of the samples. The probability of annual infection with HAdV and EC was, in the worst situation, 100% and 1.3%, respectively. Regarding the qualitative and quantitative aspects, there was a significant positive correlation between the absence of EC and the withdrawal of water from the cistern using a pump and the opposite when the withdrawal was carried out using a bucket or hose. Based on the results found, it is important to carry out actions aimed at improving water quality and, consequently, the quality of life of people living in the study community.