Impact of Drip Irrigation Method,Soil, and Virus Type on Tomato and Cucumber Contamination

The goal of this study was to better quantify the degree of viral contamination of tomato and cucumber in relationship to virus type, soil type, and irrigation method. Tomatoes and cucumbers were grown in ten-gallon (37.8 L) buckets filled with Pima clay loam or Brazito sandy loam soils. Plants were irrigated with secondary wastewater effluent using surface drip irrigation or subsurface drip irrigation. At specified time intervals irrigation water was seeded with bacteriophages MS-2 and P22, poliovirus type 1 (PV1), enteric adenovirus 40 (Ead 40), and hepatitis A virus. Surface drip irrigation always resulted in viral contamination of both the above and below ground parts of both crops. The roots showed the greatest level of contamination, followed by leaves and fruits. In contrast, with subsurface drip irrigation no viruses were detected in any of the above ground plant surfaces. It was found that under similar soil type and irrigation method, risk of crop contamination was similar for all of the viruses studied. It can be concluded that method of irrigation is the single most critical factor in the contamination trend of different parts of crop plants. Plant parts can be categorized into three groups (root, stem, and leaf/fruit) based on the risk of viral contamination from irrigation water.     

Environmental Conditions Leading to Shellfish Contamination and Related Outbreaks

Human fecal wastes contain a large variety of viruses that can enter the environment through discharge of waste materials from infected individuals. Despite the high diversity of viruses that are introduced into the environment by human fecal pollution, only a few have been recognized to cause disease in association with consumption of contaminated shellfish. To explain bivalve mollusks contamination, several factors including human epidemiology, virus persistence through sewage treatment plant, and shellfish uptake may be suggested. Considering different outbreaks described in the literature, the most common route for transmission is accidental contamination after heavy rainfall, when extra loads cause an overflow, and release of untreated sewage into the aquatic environment. Outbreak analysis also demonstrates the impact on shellfish consumption of some viral strain transmission and thus their impact on molecular epidemiology, especially for norovirus. To limit shellfish contamination and thus to protect the consumer, the most desirable and effective option is to reduce the viral input.     

Virological Quality of Irrigation Water in Leafy Green Vegetables and Berry Fruits Production Chains

This study condenses data acquired during investigations of the virological quality of irrigation water used in production of fresh produce. One hundred and eight samples of irrigation water were collected from five berry fruit farms in Finland (1), the Czech Republic (1), Serbia (2), and Poland (1), and sixty-one samples were collected from three leafy green vegetable farms in Poland, Serbia, and Greece. Samples were analyzed for index viruses of human or animal fecal contamination (human and porcine adenoviruses, and bovine polyoma viruses), and human pathogenic viruses (hepatitis A virus, hepatitis E virus, and noroviruses GI/GII). Both index and pathogenic viruses were found in irrigation water samples from the leafy green vegetables production chain. The data on the presence of index viruses indicated that the highest percentage of fecal contamination was of human origin (28.1 %, 18/64), followed by that of porcine (15.4 %, 6/39) and bovine (5.1 %, 2/39) origins. Hepatitis E virus (5 %, 1/20) and noroviruses GII (14.3 %, 4/28) were also detected. Samples from berry fruit production were also positive for both index and pathogenic viruses. The highest percentage of fecal contamination was of human origin (8.3 %, 9/108), followed by that of porcine, 4.5 % (4/89) and bovine, 1.1 % (1/89) origins. Norovirus GII (3.6 %, 2/56) was also detected. These data demonstrate that irrigation water used in primary production is an important vehicle of viral contamination for fresh produce, and thus is a critical control point which should be integrated into food safety management systems for viruses. The recommendations of Codex Alimentarius, as well as regulations on the use of water of appropriate quality for irrigation purposes, should be followed.     

病毒在土壤中的存活时间与传播能力及其影响因素

土壤是病毒在自然界主要的分布场所,也是病毒传播的一种媒介.对流感病毒、肠道病毒、甲型肝炎病毒和冠状病毒在土壤中的存活与传播进行了系统分析,并探究了病毒在土壤中吸附与存活的主要影响因素.结果表明:流感病毒、肠道病毒、甲型肝炎病毒和冠状病毒均能在土壤中存活较长时间,并能以土壤为介质进行传播,进而导致人体暴露;土壤微生物、含水量、土壤类型及温度是影响病毒在土壤中吸附与存活的主要因素,土壤微生物的存在、含水量的降低以及温度的升高可能阻碍病毒在土壤中的存活,黏粒含量及pH较高的土壤中病毒的吸附量与存活率较高,而金属氧化物及有机质含量较高的土壤中病毒的吸附量与存活率较低.基于上述分析,对病毒在土壤中存活与传播的研究提出了有针对性的建议,如系统开展我国土壤病毒的调查研究,加强病毒在土壤中存活、传播规律及影响因素的研究等.研究显示,土壤在病毒的环境传播过程中具有重要作用,不可忽视病毒经土壤传播产生的风险.      

Survival of Human Adenovirus 41 in Land-Applied Manure and Biosolids

Human Adenovirus 41 (Ad41) is an important human enteric pathogen and widely prevalent in the environment. The aim of this study was to assess the survival of Ad41 based on genome stability and infectivity in different types of manure and three types of biosolids. For viral survival studies, Ad41 was added to pelletized poultry litter (PL), alum-treated poultry litter (AL), raw poultry litter (RPL), liquid dairy manure (DM), swine manure (SM), and three types of biosolids 1, 2, 3. All samples were stored at 20 or 4°C and analyzed every 10 days for up to 60 days. Quantification PCR (qPCR) standard curves were generated for PL, AL, biosolids 1, and DM to measure the number of viral genomic copies remaining in the samples. To study the infectivity, all contaminated manure/biosolids samples were added to mammalian cell culture and viral mRNA was detected using one-step RT–PCR. Overall, Ad41 viral genomes were stable at both 20 and 4°C and there was no significant loss of viral DNA after 60 days in PL, AL, biosolids type 1, and DM. However, infectivity was lost almost immediately in high pH biosolids type 2 and 3, and infectivity decreased quickly in DM, with estimated T90 of 4.3 and 8.7 days at 20 and 4°C, respectively. Ad41 had ~1.9 log loss of infectivity after added in SM and biosolids type 1 at day 0, and estimated T90 was 12.5 and 28.6 days for biosolids type 1, and 19.1 and 51.0 days for SM at 20 and 4°C, respectively. Ad41 maintained infectivity in all three poultry litter, and after 60 days incubation, there were significantly more infectious virus in PL, AL, and RPL than biosolids 1, SM, and DM at 20°C.     

环境因素对病毒在水体中生存与传播的影响

目前,新型冠状病毒（2019-nCoV）在全球范围内广泛传播.2019-nCoV在粪便和污水中的检出揭示了病毒介水传播的可能性.了解各类环境因素对水源性病毒生存与传播的影响对介水传染病的防控及病毒风险评估具有重要意义.通过对国内外相关研究的文献调研,探究了影响病毒在水体中生存与传播的主要环境因素.研究表明,致病病毒在水环境中的存活和传播潜力与紫外线照射、水体温度、pH、盐度以及水体中存在的微生物和悬浮颗粒物等环境条件密切相关.即:①低温能够大幅延长病毒的存活时间,更有利于病毒在水体中的传播;高温能够加速病毒失活从而削弱病毒的传播潜力.②紫外线照射通过破坏病毒核酸能够有效去除和灭活病毒.③水体中的微生物能够产生对病毒颗粒不利的代谢物,或利用病毒衣壳作为营养来源,从而导致病毒失活.④各类水体中存在的大量悬浮颗粒物对病毒的吸附大大延长了病毒的存活时间,从而增强了病毒在水体中的潜在传播能力;此外,悬浮颗粒物能够促进或阻碍病毒在多孔介质中的传输与滞留.⑤pH通过改变病毒颗粒的表面电荷,影响病毒的团聚,从而影响病毒在水环境中的持久性.⑥无机离子通过影响病毒的团聚和吸附性能,从而改变其活性.环境因素对病毒存活的影响可能因不同的病毒特性而异,因此,应进一步探讨水环境中2019-nCoV存活能力的变异性,2019-nCoV在废水和饮用水处理过程中的赋存与归趋,并对废水、娱乐水域和饮用水中的2019-nCoV进行长期监测和定量风险评估.      

A Review of Known and Hypothetical Transmission Routes for Noroviruses

Human noroviruses (NoVs) are considered a worldwide leading cause of acute non-bacterial gastroenteritis. Due to a combination of prolonged shedding of high virus levels in feces, virus particle shedding during asymptomatic infections, and a high environmental persistence, NoVs are easily transmitted pathogens. Norovirus (NoV) outbreaks have often been reported and tend to affect a lot of people. NoV is spread via feces and vomit, but this NoV spread can occur through several transmission routes. While person-to-person transmission is without a doubt the dominant transmission route, human infective NoV outbreaks are often initiated by contaminated food or water. Zoonotic transmission of NoV has been investigated, but has thus far not been demonstrated. The presented review aims to give an overview of these NoV transmission routes. Regarding NoV person-to-person transmission, the NoV GII.4 genotype is discussed in the current review as it has been very successful for several decades but reasons for its success have only recently been suggested. Both pre-harvest and post-harvest contamination of food products can lead to NoV food borne illness. Pre-harvest contamination of food products mainly occurs via contact with polluted irrigation water in case of fresh produce or with contaminated harvesting water in case of bivalve molluscan shellfish. On the other hand, an infected food handler is considered as a major cause of post-harvest contamination of food products. Both transmission routes are reviewed by a summary of described NoV food borne outbreaks between 2000 and 2010. A third NoV transmission route occurs via water and the spread of NoV via river water, ground water, and surface water is reviewed. Finally, although zoonotic transmission remains hypothetical, a summary on the bovine and porcine NoV presence observed in animals is given and the presence of human infective NoV in animals is discussed.     

Comparative Uptake of Enteric Viruses into Spinach and Green Onions

Root uptake of enteric pathogens and subsequent internalization has been a produce safety concern and is being investigated as a potential route of pre-harvest contamination. The objective of this study was to determine the ability of hepatitis A virus (HAV) and the human norovirus surrogate, murine norovirus (MNV), to internalize in spinach and green onions through root uptake in both soil and hydroponic systems. HAV or MNV was inoculated into soil matrices or into two hydroponic systems, floating and nutrient film technique systems. Viruses present within spinach and green onions were detected by RT-qPCR or infectivity assays after inactivating externally present viruses with Virkon^®. HAV and MNV were not detected in green onion plants grown up to 20 days and HAV was detected in only 1 of 64 spinach plants grown in contaminated soil substrate systems up to 20 days. Compared to soil systems, a drastic difference in virus internalization was observed in hydroponic systems; HAV or pressure-treated HAV and MNV were internalized up to 4 log RT-qPCR units and internalized MNV was shown to remain infectious. Understanding the interactions of human enteric viruses on produce can aid in the elucidation of the mechanisms of attachment and internalization, and aid in understanding risks associated with contamination events.     

不同再生水灌溉方式对土壤-辣椒系统中细菌群落多样性及病原菌丰度的影响

再生水是改善水资源布局和缓解传统水源短缺问题的一种合理且可持续的替代水源,但用于灌溉会引起土壤和作物中微生物群落结构和条件致病菌丰度变化,目前这方面的研究报道较少.本研究以辣椒为对象,设置再生水灌溉(DI)、清水和再生水混灌(MI,清水∶再生水=1∶1)、清水和再生水轮灌(RI)处理,以清水灌溉(PI)为对照,通过温室盆栽试验研究不同灌溉方式对土壤性质的影响,并基于高通量测序技术结合定量PCR方法探讨再生水灌溉下辣椒果实与根际细菌群落组成和病原菌分布丰度特征.结果表明,与清水灌溉相比,再生水直接灌溉增加了土壤EC值,而降低了pH值.16S r DNA高通量测序结果显示,在门分类水平上,Proteobacteria、Bacteroidetes、Actinobacteria和Firmicutes是辣椒果实和根际共有的主要类群,其优势菌属Pantoea、Pseudomonas、Sphingomonas、Sphingopyxis、Luteimonas和Mariniflexile的相对丰度受再生水灌溉方式的影响较大.再生水灌溉分别使辣椒果实和根际中Legionella spp.和Pseudomonas syringae丰度显著增加,并且对病原菌丰度的影响差异较大.综上所述,再生水适宜作为农业灌溉用水,但不同灌溉方式可能不同程度上引入微生物污染问题,其中特定条件致病菌和植物病原菌值得关注.     

Issues Concerning Survival of Viruses on Surfaces

Viruses are the causative agents of an estimated 60% of human infections worldwide. The most common viral illnesses are produced by enteric and respiratory viruses. Transmission of these viruses from an infected person or animal to a new host can occur via several routes. Existing studies strongly suggest that contaminated fomites or surfaces play an important role in the spreading of viral diseases. The potential of viral spreading via contaminated surfaces depends particularly on the ability of the virus to maintain infectivity whilst it is in the environment. This is affected by a combination of biological, physical and chemical factors. This review summarises current knowledge about the influence of environmental factors on the survival and spread of viruses via contaminated surfaces.     

Carbon Management in Agricultural Soils

World soils have been a major source of enrichment of atmospheric concentration of CO₂ ever since the dawn of settled agriculture, about 10,000 years ago. Historic emission of soil C is estimated at 78 ± 12 Pg out of the total terrestrial emission of 136 ± 55 Pg, and post-industrial fossil fuel emission of 270 ± 30 Pg. Most soils in agricultural ecosystems have lost 50 to 75% of their antecedent soil C pool, with the magnitude of loss ranging from 30 to 60 Mg C/ha. The depletion of soil organic carbon (SOC) pool is exacerbated by soil drainage, plowing, removal of crop residue, biomass burning, subsistence or low-input agriculture, and soil degradation by erosion and other processes. The magnitude of soil C depletion is high in coarse-textured soils (e.g., sandy texture, excessive internal drainage, low activity clays and poor aggregation), prone to soil erosion and other degradative processes. Thus, most agricultural soils contain soil C pool below their ecological potential. Adoption of recommend management practices (e.g., no-till farming with crop residue mulch, incorporation of forages in the rotation cycle, maintaining a positive nutrient balance, use of manure and other biosolids), conversion of agriculturally marginal soils to a perennial land use, and restoration of degraded soils and wetlands can enhance the SOC pool. Cultivation of peatlands and harvesting of peatland moss must be strongly discouraged, and restoration of degraded soils and ecosystems encouraged especially in developing countries. The rate of SOC sequestration is 300 to 500 Kg C/ha/yr under intensive agricultural practices, and 0.8 to 1.0 Mg/ha/yr through restoration of wetlands. In soils with severe depletion of SOC pool, the rate of SOC sequestration with adoption of restorative measures which add a considerable amount of biomass to the soil, and irrigated farming may be 1.0 to 1.5 Mg/ha/yr. Principal mechanisms of soil C sequestration include aggregation, high humification rate of biosolids applied to soil, deep transfer into the sub-soil horizons, formation of secondary carbonates and leaching of bicarbonates into the ground water. The rate of formation of secondary carbonates may be 10 to 15 Kg/ha/yr, and the rate of leaching of bicarbonates with good quality irrigation water may be 0.25 to 1.0 Mg C/ha/yr. The global potential of soil C sequestration is 0.6 to 1.2 Pg C/yr which can off-set about 15% of the fossil fuel emissions.     

生物炭和秸秆还田对咸水滴灌棉田土壤微生物群落特征及功能差异的影响

干旱区淡水资源不足,农业用水主要依赖于含盐的浅层地下水,但长期咸水灌溉会造成土壤盐分积累,土壤环境恶化,不利于作物生长.因此,在长期淡水（0.35 dS·m^-1,FW）和咸水（8.04 dS·m^-1,SW）灌溉的基础上,采用等碳量设计向土壤中添加生物炭（3.7 t·hm^-2,BC）和秸秆（6 t·hm^-2,ST）,旨在明晰生物炭和秸秆还田对盐渍化土壤理化性质及微生物群落结构的影响.结果表明,咸水灌溉显著增加土壤含水量、电导率、速效磷和全碳的含量,但显著降低了pH值和速效钾的含量.生物炭和秸秆还田均显著增加土壤含水量、速效磷、速效钾和全碳的含量,但显著降低了咸水灌溉条件下的电导率值.各处理土壤优势菌门为变形菌门、放线菌门 、酸杆菌门、绿弯菌门和芽单胞菌门.咸水灌溉显著增加芽单胞菌门和变形菌门的相对丰度,但显著降低酸杆菌门和放线菌门的相对丰度.在淡水灌溉条件下,生物炭还田显著降低绿弯菌门的相对丰度;秸秆还田显著增加变形菌门的相对丰度,但显著降低酸杆菌门、放线菌门 、绿弯菌门和芽单胞菌门的相对丰度.在咸水灌溉条件下,生物炭还田显著降低绿弯菌门和芽单胞菌门的相对丰度;秸秆还田显著增加变形菌门的相对丰度,但显著降低酸杆菌门、放线菌门 、绿弯菌门和芽单胞菌门的相对丰度.LEfSe分析表明,咸水灌溉降低了土壤微生物的潜在标志物和功能数量;咸水灌溉条件下,生物炭还田增加了土壤微生物的潜在标志物和功能数量;秸秆还田增加土壤微生物的潜在功能数量;秸秆还田增加土壤微生物的潜在标志物和功能数量.RDA结果显示,土壤微生物群落和功能结构与EC_1:5 、SWC和pH值显著相关.咸水灌溉会恶化土壤环境,不利于农业生产,其中EC_1:5 、SWC和pH值是驱动土壤微生物群落和功能结构变化的重要因子,采用生物炭和秸秆还田可减缓盐分对土壤和作物的危害,为提高农业生产力奠定基础.     

Assessment of selenium pollution in agricultural soils in the Xuzhou District, Northwest Jiangsu, China

Xuzhou City is an important base for coal production and coal-fired power. To evaluate selenium contamination in this area, we sampled agricultural soil, soil profile, irrigation water, bedrock, coal, fly ash, paddy rice, and vegetables from the north of Xuzhou City, and determined their selenium contents. The background level of selenium in the soil profile was 0.08 mg/kg. The selenium concentrations in agricultural soils and irrigation water were in the range of 0.21-4.08 mg/kg and 0.002-0.29 mg/L, respec...     

Performance Evaluation of Human-Specific Viral Markers and Application of Pepper Mild Mottle Virus and CrAssphage to Environmental Water Samples as Fecal Pollution Markers in the Kathmandu Valley,Nepal

Monitoring of environmental water is crucial to protecting humans and animals from possible health risks. Although numerous human-specific viral markers have been designed to track the presence of human fecal contamination in water, they lack adequate sensitivity and specificity in different geographical regions. We evaluated the performances of six human-specific viral markers [Aichi virus 1 (AiV-1), human adenoviruses (HAdVs), BK and JC polyomaviruses (BKPyVs and JCPyVs), pepper mild mottle virus (PMMoV), and crAssphage] using 122 fecal-source samples collected from humans and five animal hosts in the Kathmandu Valley, Nepal. PMMoV and crAssphage showed high sensitivity (90–100%) with concentrations of 4.5–9.1 and 6.2–7.0 log₁₀ copies/g wet feces (n = 10), respectively, whereas BKPyVs, JCPyVs, HAdVs, and AiV-1 showed poor performances with sensitivities of 30–40%. PMMoV and crAssphage were detected in 40–100% and 8–90%, respectively, of all types of animal fecal sources and showed no significantly different concentrations among most of the fecal sources (Kruskal–Wallis test, P > 0.05), suggesting their applicability as general fecal pollution markers. Furthermore, a total of 115 environmental water samples were tested for PMMoV and crAssphage to identify fecal pollution. PMMoV and crAssphage were successfully detected in 62% (71/115) and 73% (84/115) of water samples, respectively. The greater abundance and higher mean concentration of crAssphage (4.1 ± 0.9 log₁₀ copies/L) compared with PMMoV (3.3 ± 1.4 log₁₀ copies/L) indicated greater chance of detection of crAssphage in water samples, suggesting that crAssphage could be preferred to PMMoV as a marker of fecal pollution.

     

病毒在无生命物体表面存活时间及其影响因素分析

2020年3月11日,世界卫生组织宣布新型冠状病毒肺炎（COVID-19,简称“新冠肺炎”）疫情全球大流行.病毒性传染病在人群中的发生需具备3个相互关联的条件,即传染源、传播途径和易感人群,其中传播途径是一个关键环节.从环境传播的角度,综述了包括SARS（重症急性呼吸综合征）病毒、MERS（中东呼吸综合征）病毒等病毒在无生命物体表面的存活时间及影响因素.结果表明:包括冠状病毒在内的一些具有传染性的病毒能在多种无生命物体表面存活一定时间,进而可能通过物体表面进行环境传播,造成潜在的健康风险;物体材质、温度、湿度以及病毒载量等因素是影响病毒在无生命物体表面存活的主要因素.在上述分析的基础上,对医疗废物和生活垃圾的收集、运输、处理等过程提出了针对性的防控措施,以期对新型冠状病毒（2019-nCoV）以及未来可能出现的其他病毒的环境传播防控对策提供参考.      

污灌区农田土壤环境质量评价

分别利用主成分分析法和内梅罗污染指数法对取自鞍山的6种不同类型农田(弃耕地、旱田、菜田、大棚、污灌稻田和清灌稻田)的土壤环境质量进行评价.结果表明,农田种植和灌溉方式的不同会在区域农田土壤污染物含量和土壤环境质量上表现出较明显的差异性.6种类型农田中,弃耕地的土壤环境质量最好,以下依次是菜田、旱田、清灌稻田和大棚,污灌稻田的土壤环境质量最差.利用内梅罗污染指数法和主成分分析法对6种类型农田土壤的评价结果基本一致,除菜田和旱田的排序结果略有不同外,对其他4种类型农田土壤环境质量的评价结果完全一致.主成分分析法可以用于土壤环境质量评价和土壤污染物的定量化识别.      

鞍山市城郊污灌区农地污染状况分析与评价

土壤是人类赖以生存的自然资源,它能把大量有机物最终分解为二氧化碳和水,以及各种土壤基肥的其他组成部分,但当施入的废弃物超过土壤的自净力时,就会破坏土壤的正常机能,使之失去自然生态平衡,从而严重影响农作物的产量和品质。文章主要就鞍山市城郊污灌区的农地重金属与农药污染状况作出分析与评价,并利用趋势面分析的方法得出污染的源地,以期为鞍山市污灌区的环境整治工作提供借鉴。     

Comprehensive Study on Enteric Viruses and Indicators in Surface Water in Kyoto,Japan, During 2014–2015 Season

Certain enteric viruses that are present in the water environment are potential risk factors of waterborne infections. To better understand the impact of viruses in water, both enteric viruses and their potential indicators should be comparatively investigated. In this study, occurrences of GI- and GII-noroviruses (NoVs), sapovirus (SaV), rotavirus (RoV), Aichi virus 1 (AiV-1), enterovirus (EV), and pepper mild mottle virus (PMMoV) were quantitatively determined in surface water samples in Japan. Additionally, the genotype distribution of GI- and GII-NoVs was determined using a next-generation amplicon sequencing. PMMoV was the most abundant virus regardless of season and location, indicating its usefulness as an indicator for the viral contamination of water. Other potential indicators, AiV and EV, were less abundant than GII-NoV. Viruses other than PMMoV showed seasonality, i.e., EV and other viruses (NoVs, SaV, RoV, and AiV-1) became prevalent during summer and winter, respectively. SaV showed a relatively high abundance at a location that was affected by untreated wastewater. Regarding NoV genotypes, GI.1, GI.2, GI.4, GI.5, GI.6, GII.3, GII.4, GII.6, and GII.17 were found from the surface water samples. GII.4 and GII.17 seemed to have contributed to the high abundance of GII-NoV in the samples. Interestingly, GII.17 strains became prevalent in the water samples before becoming prevalent among gastroenteritis patients in Japan. These findings provide further insights into the properties of viruses as contaminants in the water environment.     

Human-, Ovine-, and Bovine-Specific Viral Source Tracking Tools to Discriminate Between the Major Fecal Sources in Agricultural Waters

This study evaluated the sources of fecal contamination in different river catchments, using a combination of microbial source tracking tools, for human, ruminant, ovine and bovine livestock, in order to define appropriate water management strategies. Every source of waterway pollution was evaluated in river water samples from one urban river catchment and two important farming regions in New Zealand. Fecal pollution was initially measured by testing Escherichia coli and evaluating the presence of human- and ruminant-associated DNA markers of Bacteroidales (BiAdo, BacHum-UCD, BacH, and BacR) and human and ruminant fecal sterols/stanols ratios. Then specific fecal pollution sources were assessed with previously reported quantitative PCR assays targeting human-, bovine-, and ovine-specific viruses: human adenoviruses (HAdV), human JC polyomaviruses, bovine polyomaviruses (BPyV), and ovine polyomaviruses (OPyV). High level of ruminant fecal contamination was detected all over the farming areas, whereas no ruminant sources were identified in the urban river sampling sites. BacR was the most frequently observed ruminant marker and OPyV and BPyV allowed the identification of ovine and bovine fecal sources. The human fecal viral marker (HAdV) was the most frequently observed human marker, highly abundant in the urban sites, and also present in farming areas. This is the first study using simultaneously the ovine and the bovine viral markers to identify and quantify both bovine and ovine fecal pollution.