Human Pathogenic Viruses Research Articles

Antimicrobial Resistance and Bacteriophages: An Overlooked Intersection in Water Disinfection

This article focuses on how bacteriophages (phages), antibiotic-resistance genes (ARGs), and disinfection practices intersect. Phages are considered to be the most abundant biological entities on Earth and they have the potential to transfer genes (including ARGs) among their bacterial hosts. In the urban water cycle, phages are used as indicators of fecal pollution and surrogates for human viral pathogens but they are also known to withstand common disinfection treatments deployed to produce safe drinking/reclaimed water. Recent studies also suggest that phages have the potential to become an additional footprint to monitor water safety. A precautionary approach should therefore include phages in surveillance programs aimed at monitoring antimicrobial resistance (AMR) in the urban water cycle. This article argues that phages ought to be used to assess the efficiency of disinfection treatments (both classical and novel) on reducing the risk associated with antibiotic resistance. Finally, this article discusses contributions to the advancement of AMR stewardship in aquatic settings and is relevant for researchers and water industry practitioners.

Prevalence of anti-herpes simplex virus type 1 among dental students of Birjand University of Medical Sciences, Iran, 2017-2018: Short Communication

Herpes simplex virus is considered one of the most common human infections in most parts of the world, among which, herpes simplex virus 1 (HSV-1) is one of the most important human pathogenic viruses that cause numerous skin and oral lesions. Practitioners of the dental profession and related fields are in close contact with numerous patients referring to dental clinics and are at risk of cross-infection. Regarding this, one of the infections that dental professionals are exposed to is herpes simplex virus infection. This study aimed to evaluate the level of HSV1 antibody among dental students of Birjand in 2018-2019. This cross-sectional study was performed on 100 dental students of Birjand University of Medical Sciences, Iran. After obtaining informed consent, a peripheral blood sample (5 ml) was collected from participants and the presence of anti-virus antibody was examined using an Anti-Herpes-1 IgG kit with the enzyme-linked immunosorbent assay. It was revealed that 41% of the subjects had anti-herpes type 1 antibodies. Based on data analysis, the prevalence of HSV1 antibody was higher in pre-clinical and clinical level than in basic science; however, there was no significant relationship between students' educational level and antibody prevalence.

Compuestos bioactivos de hongos con actividades antivirales: Mecanismos de acción y rutas biosintéticas

Viral infections have affected human health, causing critical pandemics and mortality worldwide. Viruses can also cause enormous economic problems for society globally. Bioactive compounds isolated from fungi (both edible and nonedible) have shown potential activity against viruses. In this review, we describe the fungal natural compounds that have exhibited capability to inhibit some human pathogenic viruses, such as human immunodeficiency virus, dengue virus, herpes simplex virus, bovine herpes virus, influenza virus, respiratory syndrome virus, hepatitis virus among others. We focused on the biosynthetic pathways of fungal bioactive compounds and addressed the current knowledge about their antiviral mechanisms of action and specific targets. Fungal bioactive compounds are able to inhibit viral reproduction, blocking viral penetration, replication or translation as well as integrase or protease action. Fungal compounds able to inhibit protease such as. ganodermatriol, ergosterol, terpenoids, ganoderic acid GS-2, ganoderiol, sterigmatocystin, emericellin, cordycepin, ergosterol peroxide, myristic acid among others, may have a significant value to society at present, as they may have the potential to treat severe viral respiratory infections. Fungi represent a potential natural source of bioactive molecules that can be exploited for treating viral infections, which represent one of the main causes of disease worldwide. However, extensive investigations on clinical trials are required for the introduction of new antiviral agents into the market.

Molecular and clinical characteristics related to rhinovirus infection in Brasília, Brazil.

IntroductionHuman rhinovirus (HRV) is one of the most common human viral pathogens related to infections of the upper and lower respiratory tract, which can result in bronchiolitis and pneumonia. However, the relevance of HRV in human health was under-estimated for long time due to the absence of molecular targets for influenza and influenza-like syndrome surveillance in Brasília, Brazil. ObjectivesThe main objective of this study was analyze the clinical characteristics and outcomes of HRV infections in comparison with patients without HRV and other common respiratory viruses.Materials and MethodsFor this purpose, new specific primer sets were designed based on the high throughput sequencing analysis in previous study. These primers were used for HRV detection by RT-qPCR and Sanger sequencing of amplified cDNA of 5′ genomic region. The phylogenetic tree with representative HRV isolates was constructed using the Mega X software. Statistical analysis considering the patient profiles were performed using IBM SPSS program with non-parametric tests.ResultsThe most prevalent virus in negative samples was rhinovirus (n = 40), including three rhinovirus species (rhinovirus A, B, and C). The odds ratio associated with HRV infection was 2.160 for patients younger than 2 years and 4.367 for people living in rural areas. The multiple analysis showed lower chance of patients with HRV presenting respiratory distress.ConclusionIn this study, it was reported the predominance of rhinoviruses in cases of respiratory illness for negative patients for the influenza and influenza-like syndrome surveillance, being rhinorrhea, the most significant symptom associated with the disease.Supplementary InformationThe online version contains supplementary material available at 10.1007/s42770-020-00411-0.

An Ebola, Neisseria and Trypanosoma human protein interaction census reveals a conserved human protein cluster targeted by various human pathogens

Filovirus ebolavirus (ZE; Zaire ebolavirus, Bundibugyo ebolavirus), Neisseria meningitidis (NM), and Trypanosoma brucei (Tb) are serious infectious pathogens, spanning viruses, bacteria and protists and all may target the blood and central nervous system during their life cycle. NM and Tb are extracellular pathogens while ZE is obligatory intracellular, targetting immune privileged sites. By using interactomics and comparative evolutionary analysis we studied whether conserved human proteins are targeted by these pathogens. We examined 2797 unique pathogen-targeted human proteins. The information derived from orthology searches of experimentally validated protein–protein interactions (PPIs) resulted both in unique and shared PPIs for each pathogen. Comparing and analyzing conserved and pathogen-specific infection pathways for NM, TB and ZE, we identified human proteins predicted to be targeted in at least two of the compared host-pathogen networks. However, four proteins were common to all three host-pathogen interactomes: the elongation factor 1-alpha 1 (EEF1A1), the SWI/SNF complex subunit SMARCC2 (matrix-associated actin-dependent regulator of chromatin subfamily C), the dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 (RPN1), and the tubulin beta-5 chain (TUBB). These four human proteins all are also involved in cytoskeleton and its regulation and are often addressed by various human pathogens. Specifically, we found (i) 56 human pathogenic bacteria and viruses that target these four proteins, (ii) the well researched new pandemic pathogen SARS-CoV-2 targets two of these four human proteins and (iii) nine human pathogenic fungi (yet another evolutionary distant organism group) target three of the conserved proteins by 130 high confidence interactions.

Reliable Generation of Glial Enriched Progenitors from Human Fibroblast-Derived iPSCs

White matter stroke (WMS) occurs as small infarcts in deep penetrating blood vessels in the brain and affects the regions of the brain that carry connections, termed the subcortical white matter. WMS progresses over years and has devastating clinical consequences. Unlike large grey matter strokes, WMS disrupts the axonal architecture of the brain and depletes astrocytes, oligodendrocyte lineage cells, axons and myelinating cells, resulting in abnormalities of gait and executive function. An astrocytic cell-based therapy is positioned as a strong therapeutic candidate after WMS. In this study we report, the reliable generation of a novel stem cell-based therapeutic product, glial enriched progenitors (GEPs) derived from human induced pluripotent stem cells (hiPSCs). By transient treatment of hiPSC derived neural progenitors (hiPSC-NPCs) with the small molecule deferoxamine, a prolyl hydroxylase inhibitor, for three days hiPSC-NPCs become permanently biased towards an astrocytic fate, producing hiPSC-GEPs. In preparation for clinical application, we have developed qualification assays to ensure identity, safety, purity, and viability of the cells prior to manufacture. Using tailored q-RT-PCR-based assays, we have demonstrated the lack of pluripotency in our final therapeutic candidate cells (hiPSC-GEPs) and we have identified the unique genetic profile of hiPSC-GEPs that is clearly distinct from the parent lines, hiPSCs and iPSC-NPCs. After completion of the viability assay, we have stablished the therapeutic window of use for hiPSC-GEPs in future clinical applications (7 hours). Lastly, we were able to reliably and consistently produce a safe therapeutic final product negative for contamination by any human or murine viral pathogens, selected bacteria, common laboratory mycoplasmas, growth of any aerobes, anaerobes, yeast, or fungi and 100 times less endotoxin levels than the maximum acceptable value. This study demonstrates the reliable and safe generation of patient derived hiPSC-GEPs that are clinically ready as a cell-based therapeutic approach for WMS.

Lupeol impairs herpes simplex virus type 1 replication by inhibiting the promoter activity of the viral immediate early gene α0.

Herpes simplex virus type 1 (HSV-1) is an important human pathogenic virus. It is urgent to develop novel antiviral targets because of the limited treatment options and the emergence of drug resistant strains. In this study, we tested the antiviral activity of lupeol, a triterpenoid compound, against HSV-1 and acyclovir (ACV) resistant strains. Lupeol significantly inhibited HSV-1 (F strain) and ACV-resistant strains including HSV-1/106, HSV-1/153, and HSV-1/Blue. Lupeol activity of the HSV-1α0 and α4 promoters, therefore down regulating the expression of the α0, α4, and α27 genes. Collectively, lupeol showed strong antiviral activity against HSV-1 and ACV-resistant strains, and could be a promising therapeutic candidate for HSV-1 pathogenesis. Keywords: herpes simplex virus 1; lupeol; ACV-resistant strains; promoter.

Coronaviruses: The Most Dangerous Pathogen of Present Era

Coronaviruses are the major group of viruses belonging to the Order Nidovirales. Four families- Coronoviridae, Arteriviridae, Mesoniviridae, and Roviviridae are included in this Order. All CoVs are pleomorphic RNA viruses characterized by club-like spikes that project from their surface. These viruses have unusually large RNA genome, with a unique replication strategy. CoVs were not considered as highly pathogenic for humans until the emergence of SARS-CoV in 2002-03 in China. The emergence of another highly pathogenic CoV, Middle East Respiratory syndrome (MERS-CoV) in the Middle East Countries confirmed the occurrence of highly pathogenic human viruses among the Coronaviruses. In this article we provide a brief introduction to coronaviruses, mode of action, pathogenesis, current situation, prevention and control of COVID-19.

Antitumor/antiviral carbon quantum dots based on carrageenan and pullulan

Requirement for medication from pathogenic human viruses and cancer diseases are urgently considered, while, numerous reports were focused on investigating easily manufactured and excellently effective therapeutic reagents. Herein, CQDs were prepared with size of 2.1 nm from both of carrageenan and pullulan. CQDs nucleated from pullulan showed higher anti-proliferative effects against cancer cells, while, treatment with 100 μg/mL of CQDs colloids originated from pullulan and carrageenan separately resulted in diminishing of cancer cell viability percent to be 42.1 & 58.7%, respectively. Plaque reduction assay was also affirmed that, 2.5 μg/L of both of pullulan and carrageenan based CQDs exhibited viral inhibition with percent of 44.3& 59.5%, respectively. As a conclusion, pullulan showed seniority over carrageenan in nucleation of CQDs with higher anticancer activities. While, estimation of antiviral performance of the prepared CQDs confirmed the priority of carrageenan compared to pullulan in preparation of CQDs as antiviral laborer.

Link between Diabetes and corona virus disease – A review study

Diabetes is one of the main comorbidities related to the seriousness of every one in three known human pathogenic corona virus contaminations, including extreme intense respiratory disorder. Diabetic cases have expanded dangers in serious complexities involving Respiratory Distress Syndrome and MODS disappointment. Contingent upon worldwide district, twenty–half of cases in the Corona virus infection pandemic were diabetics. Given the significance of a connection linked corona virus disease and diabetes; we have shaped a global board of specialists amongst the branch of diabetes and endocrinology to give certain direction & functional suggestions in administration of diabetes during corona virus infection. We mean to quickly give understanding in likely robotic connections between the Corona virus illness & diabetes, current down to earth the board proposals, and expound on the various requirements of a few patient gatherings. Scant information exist with respect to glucose digestion and improvement of intense difficulties of diabetes example ketoacidosis in patients with COVID-19. Contamination of corona virus in those with diabetes potentially triggers higher pressure conditions, with more prominent arrival of hyperglycemic hormones, e.g., glucocorticoids and catecholamines, prompting expanded blood glucose levels and irregular glucose inconstancy. Then again, a review concentrate from Wuhan revealed that around 10% of the patients with type 2 diabetes mellitus and Corona virus illness endured in any event one scene of hypoglycemia less than 3.9 mmol/L. Hyperglycemia appeared to assemble favorable to fiery monocytes and increment platelet reactivity, adding to a higher cardiovascular mortality in patients with diabetes.

Understanding the outcomes of COVID-19 - does the current model of an acute respiratory infection really fit?

Although coronavirus disease 2019 (COVID-19) is regarded as an acute, resolving infection followed by the development of protective immunity, recent systematic literature review documents evidence for often highly prolonged shedding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in respiratory and faecal samples, periodic recurrence of PCR positivity in a substantial proportion of individuals and increasingly documented instances of reinfection associated with a lack of protective immunity. This pattern of infection is quite distinct from the acute/resolving nature of other human pathogenic respiratory viruses, such as influenza A virus and respiratory syncytial virus. Prolonged shedding of SARS-CoV-2 furthermore occurs irrespective of disease severity or development of virus-neutralizing antibodies. SARS-CoV-2 possesses an intensely structured RNA genome, an attribute shared with other human and veterinary coronaviruses and with other mammalian RNA viruses such as hepatitis C virus. These are capable of long-term persistence, possibly through poorly understood RNA structure-mediated effects on innate and adaptive host immune responses. The assumption that resolution of COVID-19 and the appearance of anti-SARS-CoV-2 IgG antibodies represents virus clearance and protection from reinfection, implicit for example in the susceptible–infected–recovered (SIR) model used for epidemic prediction, should be rigorously re-evaluated.

Герпесвирусы. Часть 1

One of the urgent problems of modern medicine is the high incidence of herpesvirus infections. The high prevalence of herpesviruses in the human population of the world allow us to consider herpes a common systemic disease of the whole organism. Doctors of any specialty are faced with the clinical manifestations of herpes infection in patients, and they themselves are a risk group of chronic herpes infections formation due to constant patient contacts and frequent professional psycho-emotional overload. Herpes infections are a group of infectious diseases caused by human herpesviruses. Now it is known 8 species of herpesvirus causing various human diseases that occur in the acute (during the initial contact with the infection) or chronic form. The herpesvirus family has a number of common properties that distinguish them from other human pathogenic viruses. There are three subfamilies in the Herpesviridae family. Alpha herpesviruses (Аlphaherpesvirinae) include the two serotypes of the herpes simplex virus (HSV-1 and HSV-2), and the varicella-zoster virus (herpes zoster). Beta herpesviruses (Betaherpesvirinae) include cytomegalovirus, human herpes viruses of types 6 and 7 (HHV-5, HHV-6, HHV-7). Gamma herpes viruses (Gammaherpesvirinae) include the Epstein-Barr virus, human herpesvirus type 8 (HHV-4, HHV-8). Clinical manifestations of herpes infection depend more on the immunity state of the infected organism than on the pathogenic properties of the pathogen itself, and develop only in conditions of immunodeficiency caused by various unfavorable factors. Herpesviruses are able to damage organs, weaken the body's immunity, creating conditions for the attachment of the other infections (fungal, bacterial), which in turn can cause organ damage. The herpesvirus ability to infect all organs and tissues of the body determines a significant clinical polymorphism of diseases, as well as the necessity to study various biological liquids. Herpesviruses can be transmitted from person to person by aerosol, contact, sexual and parenteral transmission, as well as from mother to fetus or newborn, they also can act as mutagens. The pathogenesis of herpesvirus infections is rather complex and not completely understood. For a proper understanding of the disease pathogenesis it is necessary to know the main stages of reproduction of human herpesviruses. Modern laboratory techniques are used for diagnosis of herpes infection and allow obtaining more complete information for an accurate diagnosis: virological method, electron microscopy method, the method of biological sample, the polymerase chain reaction methods for the detection of viral antigens, serological, immunological, cytological and histological methods. Conclusion. The high prevalence of diseases caused by herpes viruses, the complex, not fully understood pathogenesis and high contagiousness of diseases, as well as a variety of clinical manifestations of herpesvirus infections with the possibility of the formation of mixed forms with a blurred clinical picture dictate the need for a detailed study of herpes viruses and knowledge of methods for diagnosing herpes infections

Advances in Transgenic Mouse Models to Study Infections by Human Pathogenic Viruses.

Medical research is changing into direction of precision therapy, thus, sophisticated preclinical models are urgently needed. In human pathogenic virus research, the major technical hurdle is not only to translate discoveries from animals to treatments of humans, but also to overcome the problem of interspecies differences with regard to productive infections and comparable disease development. Transgenic mice provide a basis for research of disease pathogenesis after infection with human-specific viruses. Today, humanized mice can be found at the very heart of this forefront of medical research allowing for recapitulation of disease pathogenesis and drug mechanisms in humans. This review discusses progress in the development and use of transgenic mice for the study of virus-induced human diseases towards identification of new drug innovations to treat and control human pathogenic infectious diseases.

First detection of bat-borne Issyk-Kul virus in Europe

Bats have been gaining attention as potential reservoir hosts of numerous viruses pathogenic to animals and man. Issyk-Kul virus, a member of the family Nairoviridae, was first isolated in the 1970s from vespertilionid bats in Central Asia. Issyk-Kul virus has been described as human-pathogenic virus, causing febrile outbreaks in humans with headaches, myalgia and nausea. Here we describe the detection of a novel strain of Issyk-Kul virus from Eptesicus nilssonii in Germany. This finding indicates for the first time the prevalence of these zoonotic viruses in Europe.

Human Respiratory Syncytial Virus Detected in Mountain Gorilla Respiratory Outbreaks

Respiratory illness (RI) accounts for a large proportion of mortalities in mountain gorillas (Gorilla beringei beringei), and fatal outbreaks, including disease caused by human metapneumovirus (HMPV) infections, have heightened concern about the risk of human pathogen transmission to this endangered species, which is not only critically important to the biodiversity of its ecosystem but also to the economies of the surrounding human communities. Our goal was to conduct a molecular epidemiologic study to detect the presence of HRSV and HMPV in fecal samples from wild human-habituated free-ranging mountain gorillas in Rwanda and to evaluate the role of these viruses in RI outbreaks. Fecal samples were collected from gorillas with clinical signs of RI between June 2012 and February 2013 and tested by real-time and conventional polymerase chain reaction (PCR) assays; comparison fecal samples were obtained from gorillas without clinical signs of RI sampled during the 2010 Virunga gorilla population census. PCR assays detected HMPV and HRSV first in spiked samples; subsequently, HRSV-A, the worldwide-circulating ON1 genotype, was detected in 12 of 20 mountain gorilla fecal samples collected from gorillas with RI during outbreaks, but not in samples from animals without respiratory illness. Our findings confirmed that pathogenic human respiratory viruses are transmitted to gorillas and that they are repeatedly introduced into mountain gorilla populations from people, attesting to the need for stringent biosecurity measures for the protection of gorilla health.

Prediction of the incubation period for COVID-19 and future virus disease outbreaks

BackgroundA crucial factor in mitigating respiratory viral outbreaks is early determination of the duration of the incubation period and, accordingly, the required quarantine time for potentially exposed individuals. At the time of the COVID-19 pandemic, optimization of quarantine regimes becomes paramount for public health, societal well-being, and global economy. However, biological factors that determine the duration of the virus incubation period remain poorly understood.ResultsWe demonstrate a strong positive correlation between the length of the incubation period and disease severity for a wide range of human pathogenic viruses. Using a machine learning approach, we develop a predictive model that accurately estimates, solely from several virus genome features, in particular, the number of protein-coding genes and the GC content, the incubation time ranges for diverse human pathogenic RNA viruses including SARS-CoV-2. The predictive approach described here can directly help in establishing the appropriate quarantine durations and thus facilitate controlling future outbreaks.ConclusionsThe length of the incubation period in viral diseases strongly correlates with disease severity, emphasizing the biological and epidemiological importance of the incubation period. Perhaps, surprisingly, incubation times of pathogenic RNA viruses can be accurately predicted solely from generic features of virus genomes. Elucidation of the biological underpinnings of the connections between these features and disease progression can be expected to reveal key aspects of virus pathogenesis.

Antibody Conjugated Nanocarriers for Targeted Antibiotic Delivery: Application in the Treatment of Bacterial Biofilm Infections

Conventional antibiotic treatment is in most cases insufficient to eradicate biofilm-related infections, resulting in high risk of treatment failure and recurrent infections. Recent studies have shown that novel methods of antibiotic delivery can improve clinical outcomes and reduce the emergence of antibiotic resistance. The objectives of this work were to develop and evaluate a targeting nanocarrier system that enables effective delivery of antimicrobial drugs to Staphylococcus aureus, a commonly virulent human pathogen. For this purpose, we first prepared a formulation of polymeric nanoparticles suitable for encapsulation and sustained release of antibiotics. A specific antibody against S. aureus was used as targeting ligand and was covalently immobilized onto the surface of nanoparticulate materials. It was demonstrated that the targeting nanoparticles preferentially bound S. aureus cells and presented an elevated accumulation in S. aureus biofilm. Compared to free form antibiotic, the antibiotic-loaded targeting nanoparticles significantly enhanced in vitro bactericidal activity against S. aureus both in planktonic and biofilm forms. Using a mouse infection model, we observed improved therapeutic efficacy of these antibiotic-loaded nanoparticles after a single intravenous administration. Taken together, our studies show that the targeting nanoparticulate system could be a promising strategy to enhance the biodistribution of antibiotics and thereby improve their efficacy.

Antiviral drugs targeting endosomal membrane proteins inhibit distant animal and human pathogenic viruses

The endocytic pathway is a common strategy that several highly pathogenic viruses use to enter into the cell. To demonstrate the usefulness of this pathway as a common target for the development of broad-spectrum antivirals, the inhibitory effect of drug compounds targeting endosomal membrane proteins were investigated. This study entailed direct comparison of drug effectiveness against animal and human pathogenic viruses, namely Ebola (EBOV), African swine fever virus (ASFV), and the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).A panel of experimental and FDA-approved compounds targeting calcium channels and PIKfyve at the endosomal membrane caused potent reductions of entry up to 90% in SARS-CoV-2 S-protein pseudotyped retrovirus. Similar inhibition was observed against transduced EBOV glycoprotein pseudovirus and ASFV. SARS-CoV-2 infection was potently inhibited by selective estrogen receptor modulators in cells transduced with pseudovirus, among them Raloxifen inhibited ASFV with very low 50% inhibitory concentration. Finally, the mechanism of the inhibition caused by the latter in ASFV infection was analyzed.Overall, this work shows that cellular proteins related to the endocytic pathway can constitute suitable cellular targets for broad range antiviral compounds.

Ionophore antibiotic X-206 is a potent inhibitor of SARS-CoV-2 infection in vitro

Pandemic spread of emerging human pathogenic viruses, such as the current SARS-CoV-2, poses both an immediate and future challenge to human health and society. Currently, effective treatment of infection with SARS-CoV-2 is limited and broad spectrum antiviral therapies to meet other emerging pandemics are absent leaving the World population largely unprotected. Here, we have identified distinct members of the family of polyether ionophore antibiotics with potent ability to inhibit SARS-CoV-2 replication and cytopathogenicity in cells. Several compounds from this class displayed more than 100-fold selectivity between viral-induced cytopathogenicity and inhibition of cell viability, however the compound X-206 displayed >500-fold selectivity and was furthermore able to inhibit viral replication even at sub-nM levels. The antiviral mechanism of the polyether ionophores is currently not understood in detail. We demonstrate, e.g. through unbiased bioactivity profiling, that their effects on the host cells differ from those of cationic amphiphiles such as hydroxychloroquine. Collectively, our data suggest that polyether ionophore antibiotics should be subject to further investigations as potential broad-spectrum antiviral agents.

Application of Capsid Integrity (RT-)qPCR to Assessing Occurrence of Intact Viruses in Surface Water and Tap Water in Japan

Capsid integrity (RT-)qPCR has recently been developed to discriminate between intact forms from inactivated forms of viruses, but its applicability to identifying integrity of viruses in drinking water has remained limited. In this study, we investigated the application of capsid integrity (RT-)qPCR using cis-dichlorodiammineplatinum (CDDP) with sodium deoxycholate (SD) pretreatment (SD-CDDP-(RT-)qPCR) to detect intact viruses in surface water and tap water. A total of 63 water samples (surface water, n = 20; tap water, n = 43) were collected in the Kanto region in Japan and quantified by conventional (RT)-qPCR and SD-CDDP-(RT-)qPCR for pepper mild mottle virus (PMMoV) and seven other viruses pathogenic to humans (Aichivirus (AiV), noroviruses of genotypes I and II, enterovirus, adenovirus type 40 and 41, and JC and BK polyomaviruses). In surface water, PMMoV (100%) was more frequently detected than other human pathogenic viruses (30%–60%), as determined by conventional (RT-)qPCR. SD-CDDP-(RT-)qPCR also revealed that intact PMMoV (95%) was more common than intact human pathogenic viruses (20%–45%). In the tap water samples, most of the target viruses were not detected by conventional (RT-)qPCR, except for PMMoV (9%) and AiV (5%). PMMoV remained positive (5%), whereas no AiV was detected when tested by SD-CDDP-(RT-)qPCR, indicating that some PMMoV had an intact capsid, whereas AiV had damaged capsids. The presence of AiV in the absence of PMMoV in tap water produced from groundwater may demonstrate the limitation of PMMoV as a viral indicator in groundwater. In addition to being abundant in surface water, PMMoV was detected in tap water, including PMMoV with intact capsids. Thus, the absence of intact PMMoV may be used to guarantee the viral safety of tap water produced from surface water.