The proportion of global population using urban aquifers as drinking water sources increases every year and indeed the groundwater quality is not monitored adequately. Although norovirus has been identified as the first cause of groundwater-related outbreaks, the surveillance of waterborne viruses has been rather neglected. From ageing or disrupted sewer systems, occasional sewer discharges (e.g. combined sewer overflows, storm runoff), to poorly managed reclaimed water infiltration practices, multiple are the pathways that cause groundwater quality deterioration. This study revises the main viral contamination sources and the factors affecting viral contamination of groundwater bodies in terms of transport, inactivation, and survival of the viral particles. It also summarizes the methods used for those reporting the presence of human viruses in urban groundwaters. A total of 36 articles have been included in the method survey spanning a period of 24 years (1999–2022). There is a need of systematic monitoring considering representative set of waterborne pathogens. The evaluation of the presence of human adenovirus seems a useful tool to predict the presence of other waterborne pathogens in groundwater. Large volume sampling methods, but also new passive sampling methodologies applied to groundwater, coupled to target massive sequencing approaches may elucidate the range of pathogens capable of contaminating urban groundwaters for further evaluation of risk.
Citation: Rusiñol M (2023) Waterborne viruses in urban groundwater environments. PLOS Water 2(8): e0000168. https://doi.org/10.1371/journal.pwat.0000168
Editor: Mohan Amarasiri, Kitasato Daigaku, JAPAN
Published: August 17, 2023
Copyright: © 2023 Marta Rusiñol. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This work was partially supported by the UPWATER project (101081807) financed by the EU call Horizon-CL6-2022-ZEROPOLLUTION-01 and by the Agència de Gestió d’Ajuts Universitaris i de Recerca (num exp. 2021 SGR 01312). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The author has declared that no competing interests exist.
From the total earth’s available fresh water a 98% corresponds to groundwater . The proportion of the global population using safely managed services increases every year but it is estimated that still 3.6 billion people (50% of the world population that uses groundwater sources) lacks safely managed services and consumes contaminated water . Groundwater plays an important role in the urban areas in terms of public health. Cities alter the quality and quantity of the local aquifer systems. Leakage from the water supply system and storm drainage, generates large amounts of recharge water but also leakage from sewage systems, individual septic tanks, direct injection of inadequately treated wastewater into aquifers or accidental spills may introduce large amounts of pathogens into the urban aquifers [3–5]. Globally, the urban population using save groundwater sources increased from 57% in 2015 to 62% in 2020 . Nevertheless, there is still space for improving sanitation management that will have a profound impact on the quality of groundwater, particularly when sewage contaminates drinking-water sources.
A pathogen is the agent that causes disease to a host and a waterborne pathogen is the causative agent for a disease transmitted through water. The WHO Guidelines for drinking water quality  and the Global Waterborne Pathogen Project (GWPP)  have listed members of six viral families as the most important pathogens transmitted by a variety of means, including fecal-oral transmission routes. Noroviruses (NoV) and other enteric viruses, such as adenovirus (AdV), astrovirus (AstV), enterovirus (EV), hepatitis A virus (HAV) and rotavirus (RoV) are the major cause of waterborne diseases worldwide . Waterborne viral pathogens are detected in the environment because people suffering from viral infections excrete viral particles into wastewater containing feces, urine and desquamation cells. Even if wastewater is treated in a wastewater treatment facility, including secondary biological treatment, only 2 and 3 log of viruses are reduced which allows significant viral loads to be spread into the environment [8, 9].
The wastewater virome is highly diverse and so the groundwater impacted with raw or treated urban sewage [10, 11], being plant viruses and bacteriophages the most widely prevalent viruses in groundwater environments [12, 13]. A full picture of the groundwater virome can be obtained by applying untargeted viral metagenomics. When focusing on waterborne pathogens, and as observed in wastewater metagenomic analyses , Target Enrichment Sequencing (TES) and Amplicon Deep Sequencing (ADS) approaches, applied to groundwater used for irrigation, provide a more sensitive approach, allowing the detection of a diversity of viral species within a given family .
Around 30% of the disease outbreaks associated with drinking water, reported to the North American CDC’s Waterborne Disease and Outbreak Surveillance System (WBDOSS), are related to untreated groundwater . Meanwhile, in the WHO European Region about 18% of investigated outbreaks are associated with sewage contamination of groundwater sources . The main contributing factor to disease outbreaks associated with untreated groundwater seems to be human sewage  and although the majority of outbreaks have an unidentified etiology, the US Waterborne Disease and Outbreak Surveillance System (WBDOSS) indicates hepatitis A virus (HAV) as the most commonly reported etiology for outbreaks associated with untreated groundwater . Findings of a meta-analysis study, considering occurrence of viral pathogens in public-supply groundwater systems, indicate the best indicators are E.coli and somatic coliphage, although both indicators may underestimate virus occurrence . Moreover, those correlations between viral pathogens and indicators are related to the study sample size and the number of pathogen-positive detections . Thus, assessing the hazard from viruses in those settings requires knowledge on quantitative virus concentrations as well as a complete understanding on how viral contamination occurs.
1. Viral fate and contamination sources
Waterborne viruses can occur in groundwater where there is a poor soil cover, where the soil cover has been breached by the human action or when the soil has been affected by natural disasters (earthquakes, floodings). Land application of sewage effluents and sludges as well as leachates from sewerage systems or septic tanks are the main sources of waterborne virus contamination of urban groundwaters. Sewer leakage is a chronic problem for many cities worldwide due to aquifer recharge under rapid urbanization, ageing of infrastructures, insufficient maintenance and rehabilitation and in many cases poor construction materials [5, 21, 22]. There is an extensive literature assessing both infiltration and exfiltration of urban sewer systems . To this intend, flow or solute transport models as well as nitrogen isotope observations have been used to calculate that in some areas groundwater receives more than 500 liters of sewage a day . In most of the developing world, the objective of good sanitation is yet unresolved and on-site sanitation is still the most widespread mode of sanitation available . The two primary contaminants from these systems are pathogens (mainly bacteria and viruses) and nitrate.
Direct sewer discharges after an earthquake have also a great impact on groundwater supplies, but few earthquake-related studies have the focus on the microbial quality of groundwater. After the earthquakes in New Zealand-2010 , Nepal-2015 , Korea-2016  and Japan-2016  the microbial quality of groundwater changed, as well as the number of bacteria species and their abundance in the studied groundwater ecosystems. Metagenomic studies have been limited to 16S, 18S, and 23S rRNA genes and waterborne viruses have been shortly considered. Bacterial pathogens remain viable and attached to the sediments after earthquake sewage discharges  and it is assumable that waterborne viruses will do so as they have extended survival rates. Thus, viruses have the potential to reach these aquifers, perhaps at a longer travel time and in reduced concentrations posing health risks to citizens after long periods of time.
Stormwater and reclaimed water infiltration practices to promote groundwater recharge, reduce runoff during intensive rain events . However, waterborne pathogens present in stormwater have the potential to affect surrounding areas when infiltrated. Although bacterial contamination of groundwater after infiltration has been reported  few studies have examined the efficacy of infiltration practices for pathogenic organisms. In 2021 the Minnesota Department of Health published the first study charactering viruses in stormwater before and after reusing it to recharge the aquifer . The study monitored 5 waterborne viruses (AdV, EV, HAV, NoV and RoV) from 5 sampling sites across the stormwater infiltration system. RoV was detected throughout the study period in 3 out of 5 sampling sites indicating that groundwater may be susceptible to contamination by viruses when in proximity to stormwater infiltration systems, especially during periods of substantial recharge . With the prediction of more intense rain events due to climate change, sewer overflows may increase in the urban environments. Widespread evidences of sewage contamination following rainfall have been found in literature being directly related to the level of urbanization and population density [8, 34].
The urban groundwater quality has been specially studied in sub-Saharan Africa , where groundwater is the most resilient source of drinking water and indeed groundwater quality is not measured adequately. Reports of fecal contamination from eleven African countries included only one data on virus, which linked AdV and RoV contamination to pit latrine proximity . From 1948 to 2013, 649 epidemiological studies worldwide reported groundwater outbreaks. An extensive revision of all the published data, identified 17 pathogens as responsible groundwater-related outbreaks . NoV were responsible for most outbreaks followed by Campylobacter, Shigella, HAV and Giardia. Five viruses among the 17 identified pathogens were listed: NoV (39 outbreaks), HAV (21 outbreaks), RoV (2 outbreaks), AdV (1 outbreak), EV (1 outbreak), but the incidence of human enteric viruses in urban environments has been rather neglected in groundwater quality studies.
The methods used to study the virus fate in groundwater were reviewed using boolean literature searches (AND and OR) in PubMed, Google Scholar, and Web of Science. The selected search terms were groundwater, aquifer, borehole, spring, urban, cities, virus. The final algorithm as implemented in PubMed was, as example, as follows: ((“groundwater” OR “aquifer” OR “borehole” OR “spring”) AND (“urban” OR “city”) AND (“virus”)). The tool connectedpapers.com was used to fill in the gaps as it helped elucidating similar papers in the field based on co-citation and bibliographic coupling. The literature was screened to extract information on mean sample volume analyzed, concentration method, virus analyzed and incidence. Articles providing poor data on viral occurrence or method description were excluded as well as non-english literarure, studies performed under controlled conditions or using spiked viruses and focused on bacteriophages or microbial fecal indicators. Articles strongly focused on agricultural areas were finally excluded from this review to put the eye on the occurrence of human waterborne viruses. A total of 36 studies were identified, reviewed, and are summarized in Table 1 and more extensively at the supplementary information (S1 Fig).
Purple indicates that the viral DNA or RNA has been analyzed and detected and grey analyzed but not detected in any of the tested samples. AdV: adenovirus, PyV: polyomavirus, EV: enterovirus, NoV: norovirus, RoV: rotavirus, HAV and HEV: hepatitis A and E virus.
Human AdV, NoV (genogroups I and II) or EV were included in 100% of the analysis performed by the reviewed literature (Table 1) and detected in 88, 72 and 89% of the studies in which they were measured. In 44% of the revised studies, all three viruses were included. Other waterborne pathogens like RoV, Hepatitis A and E virus (HAV and HEV) were both less frequently analyzed (64, 47 and 14% of the studies respectively) and detected (65, 59, 40% of the literature in which they were included respectively) (S1 Fig). Interestingly about one of every four studies included the analysis of human polyomavirus (PyV) and detected JCPyV in 67% of the reports. This human pathogen, shed in urine by one third of healthy adults asymptomatically and highly persistent in the environment, is a good indicator of human-specific fecal contamination .
Half of the published studies reporting the presence of viruses in groundwater wells supplying drinking water have been focused in North America where specific groundwater supply types have specific rules implemented [70–72]. In the United States and Canada groundwater systems are categorized into one of three supply types: large-scale systems (supplying cities with more than 1000 inhabitants), community systems (supplying less than 1000 people), and largely untreated private domestic wells (serving single households). Although large urban systems, which are disinfected, are more likely to be adequately maintained and appropriately treated, 15% of the sources are positive for enteric pathogen, with no differences according to groundwater system type .
2. Factors affecting viral fate in groundwater bodies
Viral fate in groundwater will be affected by both physicochemical properties of soil and water and the diverse factors affecting the viral particle. Those factors will mainly rely on four processes: filtration, adsorption, survival, and die-off/inactivation.
Virus filtration and adsorption to aquifer sediments
Filtration results when the pathogens are too large to fit through the soil or aquifer pores. The extent of filtration depends on the type of soil and rocks through which groundwater flows. For example, silts are more effective at trapping viruses than sands (Fig 1).
Soil types are classified based on grain size (based on the United States Department of Agriculture classification).
Physical removal by pores is less effective for viruses than other pathogens because of the small size of viruses. The pore size of the aquifer soil influences the travel time, which can be important to consider because viruses lose their infectivity with time in the groundwater . Aquifer types are diverse, and it is difficult to stablish a direct relationship between soil materials and presence of waterborne viruses. Wallender and coworkers, reviewed and reported that 26.2% of waterborne outbreaks were associated with karst limestone bedrock, because bedrock fracturing, unconsolidated bedrock materials and thin subsoil layers may provide pathways for contamination transport . Nevertheless, the association between geology and viral contamination is not clear as different studies present diverse number of monitored wells in each aquifer type and period of time .
Adsorption occurs when the microorganisms become attached to particles and removes them from the water or at least delays their transport. Virus adsorption onto sediment grains is considered the primary removal mechanism in groundwater, with a complex dependence on the chemistry of the sediment and water. For example, wells located in sand and gravel aquifers are more likely to be virus contaminated than those in other aquifer types . Considering both filtration and adsorption factors viruses can move large distances in those scenarios, reaching depths of 67 m and horizontal migration of 408 m in glacial till and 1600 m in fractured limestone [40, 75].
Together with sediment surface charges, viral surface properties affect the degree of virus attachment during transport [76, 77]. The isoelectric point (IEP) of viral surface is used to predict the electrostatic interactions of viruses because when pH is above the IEP, the viral particles are negatively charged and will be adsorbing to positively charged soils . Groundwater pH typically ranges from 6 to 8,5 and IEP of most of the waterborne viruses is lower [78–82] (Fig 2).
Rainfall water, typically at pH7, can decrease the pH of groundwater and enhance virus transport . The same effect will occur with the organic contamination from surface runoff or sewage leachate, that by introducing nitrates (NO3-) will make pH of water to decrease. Within the saturated zone of the aquifer, it is expected the presence of divalent ions or low groundwater pH favors adhesion . It has been calculated that adhesion/aggregation of virus to soil particles are responsible for most of the viral loss in groundwater and it is important to consider that this phenomenon is reversible. If water physicochemical conditions change viral particles may be released. In opposite to divalent ions and pH, organic matter in the medium may compete with viruses for adsorption on surfaces .
Traditionally, field injection studies have used bacteriophages and there is a lack in literature of studies using viruses infecting human . Nevertheless, in lab-scale studies and using model enveloped viruses (bacteriophage ϕ6), aggregation of sediment with virus occurred regardless of mineral type . Large numbers of virions remained viable post-aggregation indicating that small-sized aggregates, which may travel more readily through porous media, may pose an infection risk. Hydrogeologic conditions of fractured bedrock aquifers may for example create wide capture zones and short groundwater travel times, leading contamination but at very low concentrations .
Virus survival and inactivation
Although viruses cannot replicate outside their hosts, waterborne viruses can survive in groundwater environments for long periods and remain infective in water. One of the first studies facing the occurrence of viruses in groundwater included cell culture assays to determine the presence of infectious viruses . This work concluded that in 21 of the 448 samples analyzed viruses were infective. Nevertheless, researchers generally use spiked viruses to produce artificially contaminated water and study viral survival which may be not representative of the real threats in the groundwater environments .
The survival of viruses in groundwater was first studied in 1982, when EV demonstrated to persist longer times (24h) than bacteria . One of the first studies assessing specific virus persistence in groundwater revealed that temperature was the only variable significantly correlated with the decay rates of two different EV (poliovirus 1 and echovirus 1) . Few years later temperature, dissolved oxygen concentration and the presence of microorganisms were also listed as factors influencing EV survival . The presence of groundwater microorganisms was then described as the most influential factor affecting the decay of viruses, while temperature, soil moisture or desiccation, adsorption to soil oxygen and nutrient levels indirectly influence virus decay by influencing the activity of the groundwater bacteria [91, 92]. Viruses typically persist longer in moist environments compared to dry conditions but also soil type seems to protect differently the viral particles due to the absorption strength. Many authors have stated that clay soils increase virus survival rates compared to sandy soils . A linear correlation is stablished between temperature and the viral decay, indicating a clear relationship between virus survival and temperature [87, 94].
Some studies have adapted the methodology and used genome quantification assays to increase sensitivity and reproducibility in the survival study results [74, 95]. Other authors have used culturable surrogates (Murine norovirus and Tulane virus) to assess the persistence of nonculturable viruses like the human norovirus [96, 97]. Human norovirus surrogates remained infectious in a cell culture assay up to 100 days of incubation and the presence of intact viral capsids enclosing the genomes (evaluated using a RNase assay coupled with RT-qPCR) was present up to 100 days after inoculation .
When considering genome detection, long-term genome persistence of NoV and AdV has been observed. Several studies using spiked AdV showed that its DNA genome can remain detectable 1343 days when stored in dark conditions at 4°C , during 385-day study at 4°C  or during a 672-day study at 12°C . Also NoV RNA genome was detectable after 1277 days  and even 3 years . Along with an increasing awareness about groundwater contamination, more information about the main factors affecting virus survival in groundwater appears in literature.
3. Methods for the surveillance of viruses in urban groundwaters
Most of the large surveillance studies (with more than 100 samples) took place in North America [4, 5, 37, 39, 42, 43, 54, 58, 63, 65, 67]. Only one study addressing frequency and patterns of viral contamination was focused in West Africa  and any of the reviewed reports and research papers from Europe or Asia included more than 40 samples (Table 1). Electropositive filtration was the primary viral concentration method used by 64% (23/36) of the authors included in this review (Fig 3) (see the detailed summary in S1 Fig).
Year of publication (from 1999 to 2022) and bibliography reference numbers are indicated in each solar slice, representing each reviewed research study. Heatmap cells contain the number of articles using a specific combination of methodologies. Colors spanned from purple (frequently used combination) to yellow (combination used in one research paper).
Potential associations between study sample size, sample volume and the percentage of virus detection (positive samples/samples analyzed) were analyzed using Pearson’s correlation coefficient tests. A weak and negative Pearson correlation coefficient (r = -0.29) was observed between the percentage of virus incidence and the number of samples analyzed. It needs to be pointed out that the studies included in this review were performed under different scenarios and include: studies performed during an outbreak investigation [41, 59], which usually consider few samples but find high percentages of incidence (>50%) and studies aiming to draw an accurate snapshot of presence of viruses in specific groundwater systems [4, 38, 63, 65]. Whatever is the aim, and as happens in clinical studies, one can draw a precise and accurate conclusion only with an appropriate sample size. A small number of samples may not give a result that enables to detect a difference between groundwater wells (e.g. aquifer types, drinking water systems). Nevertheless, a very large sample size, which may give a clearer overview of the fate of viruses, will involve higher amounts of time and resources which cannot be covered by each interested country.
Electropositive filtration, which does not typically require preconditioning of the sample, has been the gold standard method used as a primary concentration step over the first 20 years (1999–2018) of waterborne virus research in groundwater (Fig 3). Since 2019, ultrafiltration devices (e.g. Rexeed 25S and Leoceed 21H), previously used for virus concentration  and commonly used in clinical settings for hemodialysis, have been employed for sampling larger volumes of water for viruses. Viral recoveries from hollow-fiber ultrafilters are higher than those from electropositive filters and have the added benefit of being a multi-pathogen concentrator .
Regardless of the concentration methodology, the sample volume analyzed has decreased over the years among the studies examined (Fig 4). Most of the studies have been published over the second half of the studied period being HAdV detected incidence the highest compared to the incidence of other viruses analyzed. As stated in section 1, more than 80% of the literature analyzed and detected NoV as the major source of the outbreaks although the HAdV occurrence was higher in all the studies where both were analyzed. This confirms that the evaluation of the presence of HAdV could be a useful tool to predict the presence of other waterborne pathogens in groundwater.
Concentric circles represent waterborne viruses (Human adenovirus (HAdV), Enterovirus (EV), Norovirus (NoV), Rotavirus (RoV) and Hepatitis A and E viruses (HAV and HEV)) and one human fecal indicator (HPyV (Human polyomavirus)) analysed and detected in each of the revised literaure.
There is little existing literature on groundwater virome. The relatively low abundance of viral particles within groundwater systems requires cumbersome library preparation protocols to enrich viral RNA and DNA. Despite, pre-amplification protocols, studies reporting the diverse viral communities describe Myoviridae, Siphoviridae and Podoviridae as the three most dominant families in groundwater [13, 100, 101]. All three families are mainly comprised of tailed dsDNA bacteriophages that infect bacteria and archaea. In the recent years, three massive sequencing approaches (High Throughput Sequencing (HTP), Target Enrichment Sequencing (TES) and Amplicon Deep Sequencing (ADS)) have been tailored to study viruses infecting human and other vertebrates [11, 12, 14, 68, 102]. To our knowledge only one study was able to detect waterborne viruses, HAdV 41 and HEV, using a SISPA pre-amplification and a HTP sequencing approach . Avian adenoviruses and sequences related to human and bovine alpha- and gamma-herpesvirus were found in other studies mapping double stranded DNA virus from sub-Saharan urban settlements . While targeted approaches like TES, that uses biotinylated oligonucleotide probes designed to bind coding sequences of specific viral taxa known to infect vertebrates, can provide a snapshot of unexpected viral pathogens and potentially zoonotic pathogens from large volumes of water [14, 68], ADS may provide higher sensitivity for the identification of viral types or variants over specific outbreak investigation.
Waterborne viruses enter urban aquifers through multiple sources and pathways, mainly from sewer leakage (a.k.a. exfiltration) but also combined sewer overflows, urban runoff and WWTP effluent recharge areas. Although groundwater sources are considered resilient sources of drinking water, viruses (and specially norovirus) are reported as the main cause of gastrointestinal outbreaks linked to consumption of contaminated groundwater. Viral filtration, adsorption, survival, and inactivation within the aquifer are well known processes. Nevertheless, systematic studies considering a representative set of waterborne pathogens are needed in each scenario, considering that high thermal stability and long survival periods, may not mimic that of pathogens that are present due to recent contamination. There is also a limited systematic monitoring data for waterborne virus in urban groundwater with only 36 references available. Thus, viral risk assessment studies [54, 67] related to groundwater consumption are commonly performed during viral outbreaks resulting in poorly defined risks because of the limited temporal resolution. Large surveillance studies have been focused within North America, where there are specific legislations and funds to study groundwater, whereas most of the urban population using groundwater as a source is in Africa and Asia. Important knowledge gaps for a sustainable management of the groundwater sources may need large volume sample methods coupled to target massive sequencing approaches. Understanding the range of pathogens capable of contaminating groundwater is important for assessing risks. Passive sampling, as an alternative to grab sampling for the monitoring of viruses in diverse water environments , may be the key to popularize microbial quality monitoring, enabling larger sample sizes and/or higher sampling frequencies. Since the Urban Waste Water Treatment legislations do not require disinfection prior to discharge and uncontrolled discharges of sewage will continue to occur, sustainable and biobased solutions are the only way of reducing viral pathogens in the receiving groundwater bodies.
I would like to acknowledge reviewers and my lab colleagues for their critical review of the manuscript.
- 1. Mullern K. Groundwater | NGWA Home [Internet]. 2022 [cited 2022 Dec 1]. https://www.ngwa.org/
- 2. WHO\UNICEF. Progress on household drinking water, sanitation and hygiene 2000–2020: five years into the SDGs [Internet]. Joint Water Supply, & Sanitation Monitoring Programme. 2021. 1–164 p.
- 3. Wakode HB, Baier K, Jha R, Azzam R. Impact of urbanization on groundwater recharge and urban water balance for the city of Hyderabad, India. Int Soil Water Conserv Res. 2018;6(1):51–62.
- 4. Borchardt MA, Spencer SK, Kieke BA, Lambertini E, Loge FJ. Viruses in nondisinfected drinking water from municipal wells and community incidence of acute gastrointestinal illness. Environ Health Perspect 2012;120(9):1272–9. pmid:22659405
- 5. Gotkowitz MB, Bradbury KR, Borchardt MA, Zhu J, Spencer SK. Effects of Climate and Sewer Condition on Virus Transport to Groundwater. Environ Sci Technol. 2016;50(16):8497–504. pmid:27434550
- 6. WHO. Guidelines for drinking-water quality: fourth edition incorporating the firrst and second addenda. Geneva: World Health Organization; 2022.
- 7. Rusiñol M, Girones R. Summary of Excreted and Waterborne Viruses. In: Rose JB, Jiménez-Cisneros B, editors. Global Water Pathogens Project. Michigan S. Michigan: Michigan State University, E. Lansing, MI, UNESCO; 2017.
- 8. Rusiñol M, Fernandez-Cassi X, Timoneda N, Carratalà A, Abril JF, Silvera C, et al. Evidence of viral dissemination and seasonality in a Mediterranean river catchment: Implications for water pollution management. J Environ Manage. 2015;159.
- 9. Okoh A, Sibanda T, Gusha SS. Inadequately treated wastewater as a source of human enteric viruses in the environment. Int J Environ Res Public Health. 2010;7(6):2620–37. pmid:20644692
- 10. Martínez-Puchol S, Rusiñol M, Fernández-Cassi X, Timoneda N, Itarte M, Andrés C, et al. Characterisation of the sewage virome: comparison of NGS tools and occurrence of significant pathogens. Sci Total Environ. 2020;713. pmid:31955099
- 11. van de Vossenberg J, Hoiting Y, Kamara AK, Tetteh MK, Simaika JP, Lutterodt G, et al. Double-stranded DNA virus assemblages in groundwater in three informal urban settlements in sub-Saharan Africa differ from each other. ACS Environ Sci Technol Water. 2021;1(9):1992–2000.
- 12. Rusiñol M, Martínez-Puchol S, Timoneda N, Fernández-Cassi X, Pérez-Cataluña A, Fernández-Bravo A, et al. Metagenomic analysis of viruses, bacteria and protozoa in irrigation water. Int J Hyg Environ Health. 2020;224.
- 13. Hegarty B, Dai Z, Raskin L, Pinto A, Wigginton K, Duhaime M. A snapshot of the global drinking water virome: Diversity and metabolic potential vary with residual disinfectant use. Water Res. 2022;218. pmid:35504157
- 14. Itarte M, Martínez-Puchol S, Forés E, Hundesa A, Timoneda N, Bofill-Mas S, et al. Ngs techniques reveal a high diversity of rna viral pathogens and papillomaviruses in fresh produce and irrigation water. Foods. 2021;10(8). pmid:34441597
- 15. Craun GF, Brunkard JM, Yoder JS, Roberts V a, Carpenter J, Wade T, et al. Causes of outbreaks associated with drinking water in the United States from 1971 to 2006. Clin Microbiol Rev [Internet]. 2010 Jul;23(3):507–28. pmid:20610821
- 16. Kulinkina A V, Shinee E, Rafael B, Herrador G, Nygård K, Schmoll O. The situation of water-related infectious diseases in the pan-european region. 2016 [cited 2023 Feb 24]; http://www.euro.who.int/pubrequest
- 17. Wallender EK, Ailes EC, Yoder JS, Roberts VA, Brunkard JM. Contributing Factors to Disease Outbreaks Associated with Untreated Groundwater. Groundwater. 2014;52(6):886–97. pmid:24116713
- 18. Barrett C, Pape B, Benedict K, Foster M, Roberts V, Rotert K, et al. Impact of Public Health Interventions on Drinking Water-Associated Outbreaks of Hepatitis A-United States, 1971–2017 [Internet]. Vol. 68, US Department of Health and Human Services/Centers for Disease Control and Prevention. 2019. https://www.cdc.gov/mmwr/preview/mmwrhtml/
- 19. Fout GS, Borchardt MA, Kieke BA, Karim MR. Human virus and microbial indicator occurrence in public-supply groundwater systems: meta-analysis of 12 international studies. Hydrogeol J. 2017;25(4):903–19. pmid:30245581
- 20. Wu J, Long SC, Das D, Dorner SM. Are microbial indicators and pathogens correlated? A statistical analysis of 40 years of research. J Water Health. 2011;9(2):265–78. pmid:21942192
- 21. Lapworth DJ, Nkhuwa DCW, Okotto-Okotto J, Pedley S, Stuart ME, Tijani MN, et al. Qualité des eaux souterraines urbaines en Afrique sub-saharienne: état actuel et implications pour la sécurité de l’approvisionnement en eau et la santé publique. Hydrogeol J. 2017;25(4):1093–116.
- 22. Patil V, Kadam A. Problems and Perspectives of the Urban Sewage System: A Geographical Review. Res Rev Int J Multidiscip [Internet]. 2022;4(3):2815–9.
- 23. Nguyen Hong Hanh, Modelling of sewer exfiltration to groundwater in urban wastewater systems: a critical review, J. Hydrol., № 596, c. 126130.
- 24. Chisala BN, Lerner DN. Distribution of sewer exfiltration to urban groundwater. Proc Inst Civ Eng Water Manag. 2008;161(6):333–41.
- 25. Krishnan S. On-site Sanitation and Groundwater Contamination: A Policy and Technical Review INREM Foundation Anand, India (with support from Bill and Melinda Gates Foundation) [Internet]. 2011.
- 26. Gregor J, Dumbleton B, Moriarty E, Wright J. Summary of Literature Impacts of Earthquakes on Groundwater Quality Prepared as part of a Ministry of Health contract for scientific services Summary of Literature Impacts of Earthquakes on Groundwater Quality. 2012.
- 27. Uprety S, Hong PY, Sadik N, Dangol B, Adhikari R, Jutla A, et al. The Effect of the 2015 Earthquake on the Bacterial Community Compositions in Water in Nepal. Front Microbiol. 2017;8:2380. pmid:29270153
- 28. Kim H, Kaown D, Kim J, Park IW, Joun WT, Lee KK. Impact of earthquake on the communities of bacteria and archaea in groundwater ecosystems. J Hydrol. 2020 1;583.
- 29. Morimura S, Zeng X, Noboru N, Hosono T. Changes to the microbial communities within groundwater in response to a large crustal earthquake in Kumamoto, southern Japan. J Hydrol. 2020;581:124341.
- 30. Devane ML, Moriarty EM, Wood D, Webster-Brown J, Gilpin BJ. The impact of major earthquakes and subsequent sewage discharges on the microbial quality of water and sediments in an urban river. Sci Total Environ. 2014;485–486(1):666–80.
- 31. Weiss PT, LeFevre G, Gulliver JS. Contamination of Soil and Groundwater Due to Stormwater Infiltration Practices, A Literature Review. St. Anthony Falls Laboratory; 2008.
- 32. Clark SE, Pitt R. Influencing Factors and a Proposed Evaluation Methodology for Predicting Groundwater Contamination Potential from Stormwater Infiltration Activities. Water Environ Res. 2007;79(1):29–36. pmid:17290969
- 33. de Lambert JR, Walsh JF, Scher DP, Firnstahl AD, Borchardt MA. Microbial pathogens and contaminants of emerging concern in groundwater at an urban subsurface stormwater infiltration site. Sci Total Environ. 2021;775:145738. pmid:33631564
- 34. Olds HT, Corsi SR, Dila DK, Halmo KM, Bootsma MJ, McLellan SL. High levels of sewage contamination released from urban areas after storm events: A quantitative survey with sewage specific bacterial indicators. PLoS Med. 2018;15(7):1–23. pmid:30040843
- 35. Verheyen J, Timmen-Wego M, Laudien R, Boussaad I, Sen S, Koc A, et al. Detection of adenoviruses and rotaviruses in drinking water sources used in rural areas of benin, west africa. Appl Environ Microbiol. 2009;75(9):2798–801. pmid:19270143
- 36. Murphy HM, Prioleau MD, Borchardt MA, Hynds PD. Review: Epidemiological evidence of groundwater contribution to global enteric disease, 1948–2015. Hydrogeol J. 2017;25(4):981–1001.
- 37. Abbaszadegan M, Stewart P, LeChevallier M. A strategy for detection of viruses in groundwater by PCR. Appl Environ Microbiol. 1999;65(2):444–9. pmid:9925566
- 38. Abbaszadegan M, Lechevallier M, Gerba C. Occurrence of Viruses in US groundwaters. J / Am Water Work Assoc. 2003;95(9):107–20.
- 39. Fout GS, Martinson BC, Moyer MWN, Dahling DR. A multiplex reverse transcription-PCR method for detection of human enteric viruses in groundwater. Appl Environ Microbiol. 2003;69(6):3158–64. pmid:12788711
- 40. Borchardt MA, Bertz PD, Spencer SK, Battigelli DA. Incidence of enteric viruses in groundwater from household wells in Wisconsin. Appl Environ Microbiol. 2003;69(2):1172–80. pmid:12571044
- 41. Borchardt MA, Haas NL, Hunt RJ. Vulnerability of drinking-water wells in La Crosse, Wisconsin, to enteric-virus contamination from surface water contributions. Appl Environ Microbiol. 2004;70(10):5937–46. pmid:15466536
- 42. Francy DS, Bushon RN, Stopar J, Luzano EJ, Fout GS. Environmental factors and chemical and microbiological water-quality constituents related to the presence of enteric viruses in ground water from small public water supplies in southeastern Michigan. Scientific Investigations Report. 2004.
- 43. Locas A, Barthe C, Barbeau B, Carrière A, Payment P. Virus occurrence in municipal groundwater sources in Quebec, Canada. Can J Microbiol. 2007;53(6):688–94. pmid:17668028
- 44. Masciopinto C, La Mantia R, Carducci A, Casini B, Calvario A, Jatta E. Unsafe tap water in households supplied from groundwater in the Salento Region of Southern Italy. J Water Health. 2007;5(1):129–48. pmid:17402285
- 45. Gabrieli R, Maccari F, Ruta A, Panà A, Divizia M. Norovirus Detection in Groundwater. Food Environ Virol. 2009;1(2):92–6.
- 46. Cheong S, Lee CCH, Song SW, Choi WC, Lee CCH, Kim SJ. Enteric viruses in raw vegetables and groundwater used for irrigation in South Korea. Appl Environ Microbiol. 2009;75(24):7745–51. pmid:19854919
- 47. Park SH, Kim EJ, Yun TH, Lee JH, Kim CK, Seo YH et al., 2010. Human Enteric Viruses in Groundwater. Food and Environmental Virology 2(2):69–73.
- 48. Hunt RJ, Borchardt MA, Richards KD, Spencer SK. Assessment of sewer source contamination of drinking water wells using tracers and human enteric viruses. Environ Sci Technol [Internet]. 2010;44(20):7956–63. pmid:20822128
- 49. Borchardt MA, Bradbury KR, Alexander EC, Kolberg RJ, Alexander SC, Archer JR, et al. Norovirus Outbreak Caused by a New Septic System in a Dolomite Aquifer. Ground Water. 2011;49(1):85–97. pmid:20199588
- 50. Johnson TB, McKay LD, Layton AC, Jones SW, Johnson GC, Cashdollar JL, et al. Viruses and Bacteria in Karst and Fractured Rock Aquifers in East Tennessee, USA. Ground Water. 2011;49(1):98–110. pmid:20331750
- 51. Gibson KE, Schwab KJ. Detection of bacterial indicators and human and bovine enteric viruses in surface water and groundwater sources potentially impacted by animal and human wastes in Lower Yakima Valley, Washington. Appl Environ Microbiol. 2011;77(1):355–62. pmid:21075875
- 52. Gibson KE, Opryszko MC, Schissler JT, Guo Y, Schwab KJ. Evaluation of human enteric viruses in surface water and drinking water resources in southern Ghana. Am J Trop Med Hyg. 2011;84(1):20–9. pmid:21212196
- 53. Jung JH, Yoo CH, Koo ES, Kim HM, Na Y, Jheong WH, et al. Occurrence of norovirus and other enteric viruses in untreated groundwaters of Korea. J Water Health [Internet]. 2011;9(3):544–55. pmid:21976201
- 54. Lambertini E, Borchardt M a, Kieke B a, Spencer SK, Loge FJ. Risk of viral acute gastrointestinal illness from nondisinfected drinking water distribution systems. Environ Sci Technol [Internet]. 2012;46(17):9299–307. pmid:22839570
- 55. Bradbury KR, Borchardt MA, Gotkowitz M, Spencer SK, Zhu J, Hunt RJ. Source and transport of human enteric viruses in deep municipal water supply wells. Environ Sci Technol [Internet]. 2013;47(9):4096–103. pmid:23570447
- 56. Corsi SR, Borchardt MA, Spencer SK, Hughes PE, Baldwin AK. Human and bovine viruses in the Milwaukee River watershed: Hydrologically relevant representation and relations with environmental variables. Sci Total Environ 2014; 490:849–60. pmid:24908645
- 57. Hruby CE, Libra RD, Fields CL, Kolpin DW, Hubbard LE, Borchardt MR, et al. 2013 Survey of Iowa groundwater and evaluation of public well vulnerability classifications for contaminants of emerging concern.
- 58. Allen AS, Borchardt MA, Kieke BA, Dunfield KE, Parker BL. Virus occurrence in private and public wells in a fractured dolostone aquifer in Canada. Hydrogeol J. 2017;25(4):1117–36.
- 59. Kauppinen A, Pitkänen T, Miettinen IT. Persistent Norovirus Contamination of Groundwater Supplies in Two Waterborne Outbreaks. Food Environ Virol. 2018;10(1):39–50. pmid:29022247
- 60. Haramoto E. Detection of Waterborne Protozoa, Viruses, and Bacteria in Groundwater and Other Water Samples in the Kathmandu Valley, Nepal. IOP Conf Ser Earth Environ Sci. 2018;120(1):0–7.
- 61. Lutterodt G, van de Vossenberg J, Hoiting Y, Kamara AK, Oduro-Kwarteng S, Foppen JWA. Microbial groundwater quality status of hand-dug wells and boreholes in the Dodowa area of Ghana. Int J Environ Res Public Health. 2018;15(4):1–12. pmid:29649111
- 62. Jurado A, Bofill-Mas S, Vázquez-Suñé E, Pujades E, Girones R, Rusiñol M. Occurrence of pathogens in the river–groundwater interface in a losing river stretch (Besòs River Delta, Spain). Sci Total Environ. 2019;696:1–8.
- 63. Stokdyk JP, Firnstahl AD, Walsh JF, Spencer SK, de Lambert JR, Anderson AC, et al. Viral, bacterial, and protozoan pathogens and fecal markers in wells supplying groundwater to public water systems in Minnesota, USA. Water Res 2020;178:115814. pmid:32325219
- 64. Rusiñol M, Hundesa A, Cárdenas-Youngs Y, Fernández-Bravo A, Pérez-Cataluña A, Moreno-Mesonero L, et al. Microbiological contamination of conventional and reclaimed irrigation water: Evaluation and management measures. Sci Total Environ. 2020;710. pmid:31923670
- 65. Pang X, Gao T, Qiu Y, Caffrey N, Popadynetz J, Younger J, et al. The prevalence and levels of enteric viruses in groundwater of private wells in rural Alberta, Canada. Water Res [Internet]. 2021;202:117425. pmid:34284123
- 66. Sorensen JPR, Aldous P, Bunting SY, McNally S, Townsend BR, Barnett MJ, et al. Seasonality of enteric viruses in groundwater-derived public water sources. Water Res [Internet]. 2021;207:117813. pmid:34785409
- 67. Borchardt MA, Stokdyk JP, Kieke BA, Muldoon MA, Spencer SK, Firnstahl AD, et al. Sources and risk factors for nitrate and microbial contamination of private household wells in the fractured dolomite aquifer of northeastern wisconsin. Environ Health Perspect. 2021;129(6):1–18. pmid:34160249
- 68. Forés E, Rusiñol M, Itarte M, Martínez-Puchol S, Calvo M, Bofill-Mas S. Evaluation of a virus concentration method based on ultrafiltration and wet foam elution for studying viruses from large-volume water samples. 829 (2022) 154431.
- 69. Bofill-Mas S. Polyomavirus. Water Sanit 21st Century Heal Microbiol Asp Excreta Wastewater Manag (Global Water Pathog Proj. 2019
- 70. USEPA. National Primary Drinking Water Regulations: Ground Water Rule [Internet]. Federal Register 2006 p. 65574–660.
- 71. USEPA. National Primary Drinking Water Regulations: Total Coliform Rule. Federal Register 2013 p. 27543–69.
- 72. Ravenscroft P, Lytton L. Seeing the Invisible: A Strategic Report on Groundwater Quality. OpenKnowledge.worldbank.org. 2022.
- 73. Hynds PD, Thomas MK, Pintar KDM. Contamination of groundwater systems in the US and Canada by enteric pathogens, 1990–2013: A review and pooled-analysis. PLoS One. 2014;9(5). pmid:24806545
- 74. Ogorzaly L, Bertrand I, Paris M, Maul A, Gantzer C. Occurrence, survival, and persistence of human adenoviruses and F-specific RNA phages in raw groundwater. Appl Environ Microbiol. 2010;76(24):8019–25. pmid:20952644
- 75. Keswick BH, Gerba CP. Viruses in groundwater. Environ Sci Technol. 1980;14(11):1290–7.
- 76. Gerba CP. Applied and Theoretical Aspects of Virus Adsorption to Surfaces. Adv Appl Microbiol. 1984;30(C):133–68. pmid:6099689
- 77. Dowd SE, Pillai SD, Wang S, Corapcioglu MY. Delineating the specific influence of virus isoelectric point and size on virus adsorption and transport through sandy soils. Appl Environ Microbiol. 1998;64(2):405–10. pmid:9464373
- 78. Michen B, Graule T. Isoelectric points of viruses. J Appl Microbiol. 2010;109(2):388–97. pmid:20102425
- 79. Zhao Q, Tian Y, Liu L, Jiang Y, Sun H, Tan S, et al. The Genomic and Genetic Evolution Analysis of Rabbit Astrovirus. Vet Sci. 2022;9(11):1–9. pmid:36356080
- 80. Heffron J, Mayer BK. Virus Isoelectric Point Estimation: Theories and Methods. Appl Environ Microbiol. 2021;87(3):1–17. pmid:33188001
- 81. Gutierrez L, Li X, Wang J, Nangmenyi G, Economy J, Kuhlenschmidt TB, et al. Adsorption of rotavirus and bacteriophage MS2 using glass fiber coated with hematite nanoparticles. Water Res. 2009;43(20):5198–208. pmid:19766286
- 82. Kapoor V, Smith C, Santo Domingo JW, Lu T, Wendell D. Correlative assessment of fecal indicators using human mitochondrial DNA as a direct marker. Environ Sci Technol. 2013;47(18):10485–93. pmid:23919424
- 83. Hunt RJ, Johnson WP. Transport de pathogènes dans les systèmes aquifères: contrastes avec le transports traditionnel de solutés. Hydrogeol J. 2017;25(4):921–30.
- 84. Gassilloud B, Gantzer C. Adhesion-aggregation and inactivation of Poliovirus 1 in groundwater stored in a hydrophobic container. Appl Environ Microbiol. 2005;71(2):912–20. pmid:15691948
- 85. Woessner WW, Ball PN, DeBorde DC, Troy TL. Viral transport in a sand and gravel aquifer underfield pumping conditions. Groundwater2. 2001;39(6):886–94.
- 86. Katz A, Peña S, Alimova A, Gottlieb P, Xu M, Block KA. Heteroaggregation of an enveloped bacteriophage with colloidal sediments and effect on virus viability. Sci Total Environ. 2018;637:104–11. pmid:29747115
- 87. Pinon A, Vialette M. Survival of viruses in water. Intervirology. 2019;61(5):214–22.
- 88. Keswick BH, Secor SL, Gerba CP, Cech I. Survival of enteric viruses and indicator bacteria in groundwater. J Environ Sci Heal Part A Environ Sci Eng. 1982;17(6):903–12.
- 89. Yates M V., Gerba CP, Kelley LM. Virus persistence in groundwater. Appl Environ Microbiol. 1985;49(4):778–81. pmid:4004211
- 90. Jansons J, Edmonds LW, Speight B, Webster A, Box PO, Hills B, et al. Survival of viruses in groundwater. Water Res. 1989;23(3):301–6.
- 91. Gordon C, Toze S. Influence of groundwater characteristics on the survival of enteric viruses. J Appl Microbiol. 2003;95(3):536–44. pmid:12911702
- 92. John DE, Rose JB. Review of factors affecting microbial survival in groundwater. Environ Sci Technol. 2005;39(19):7345–56. pmid:16245801
- 93. Parsai T, Wier MH, Miller A, Gurian PL, Kumar A. Part Four. Management of Risk From Excreta And Wastewater. In: Water and Sanitation for the 21st Century: Health and Microbiological Aspects of Excreta and Wastewater Management (Global Water Pathogen Project). 2018. p. 1–22.
- 94. Gerba CP, Choi CY. Role of irrigation water in crop contamination by viruses. In: Viruses in Foods. 2006. p. 7.
- 95. Charles KJ, Shore J, Sellwood J, Laverick M, Hart A, Pedley S. Assessment of the stability of human viruses and coliphage in groundwater by PCR and infectivity methods. J Appl Microbiol. 2009;106(6):1827–37. pmid:19298517
- 96. Fallahi S, Mattison K. Evaluation of murine norovirus persistence in environments relevant to food production and processing. J Food Prot. 2011;74(11):1847–51. pmid:22054184
- 97. Anderson-coughlin BL, Vanore A, Shearer AEH, Gartley S, Joerger RD, Sharma M, et al. Human Norovirus Surrogates Persist in Nontraditional Sources of Irrigation Water in Excess of 100 Days. J Food Prot [Internet]. 2023;86(1):100024. pmid:36916591
- 98. Seitz SR, Leon JS, Schwab KJ, Lyon GM, Dowd M, McDaniels M, et al. Norovirus infectivity in humans and persistence in water. Appl Environ Microbiol. 2011;77(19):6884–8. pmid:21856841
- 99. Cashdollar JL, Wymer L. Methods for primary concentration of viruses from water samples: a review and meta-analysis of recent studies. J Appl Microbiol. 2013;115(1):1–11. pmid:23360578
- 100. Kallies R, Hölzer M, Toscan RB, da Rocha UN, Anders J, Marz M, et al. Evaluation of sequencing library preparation protocols for viral metagenomic analysis from pristine aquifer groundwaters. Viruses. 2019;11(6). pmid:31141902
- 101. Zaouri N, Jumat MR, Cheema T, Hong PY. Metagenomics-based evaluation of groundwater microbial profiles in response to treated wastewater discharge. Environ Res. 2020;180:108835. pmid:31655333
- 102. Smith RJ, Jeffries TC, Roudnew B, Seymour JR, Fitch AJ, Simons KL, et al. Confined aquifers as viral reservoirs. 2013;5:725–30.
- 103. Mejías-Molina C, Pico-Tomàs A, Beltran-Rubinat A, Martínez-Puchol S, Corominas L, Rusiñol M, et al. Effectiveness of passive sampling for the detection and genetic characterization of human viruses in wastewater. Environ. Sci.: Water Res. Technol., 2023, 9, 1195–1204.