Analysis of adenoviruses and polyomaviruses quantified by qPCR as indicators of water quality in source and drinking-water treatment plants

Three drinking-water treatment plants were analyzed for the presence of human adenoviruses (HAdV) and JC polyomavirus (JCPyV), previously suggested as viral contamination indicators, in order to define their water quality in relation to the presence of viral pathogens and the efficiency of the treatments applied. The 90% of the river water samples had positive results of HAdV (10(1)-10(4) genome copies (GC)/L); and 48%, of JCPyV (10(0)-10(3)GC/L). Lower concentrations of HAdV and JCPyV were found in different treatment steps of the plants in absence of bacterial standards. Virus removal efficiencies were higher than 5 logs in plants 1 and 3 and could be quantified as >2 logs in plant 2. However, three post-chlorinated samples from plants 2 and 3 (11%) were found to be positive for HAdV by qPCR, but did not show infectivity in the cell cultures assayed. Simple methods based on the adsorption-elution of viruses from glass wool give low-cost and efficient virus recovery from source water and large-volume water samples. Quantification of JCPyV and HAdV using qPCR is useful for evaluating virus removal efficiency in water treatment plants, identification of Hazard Analysis and Critical Control Points (HACCP) and as a molecular index of the virological quality of water. Though infectivity is not guaranteed when using qPCR techniques in water treated with disinfection processes, the quality of source water, where viruses have proved to have infective capabilities, and the removal efficiency of viral particles may be efficiently quantified.

Human polyomaviruses, WU and KI in HIV exposed children with acute lower respiratory tract infections in hospitals in South Africa

BACKGROUND

The importance of two recently identified polyomaviruses, WUV and KIV, as respiratory pathogens in populations with a high HIV prevalence needs to be defined, since human polyomaviruses can cause significant morbidity and mortality in patients with immunosuppression. Geographic distribution and disease association of WUV and KIV genotypes are not yet clearly defined.

OBJECTIVES

To investigate the prevalence of WUV and KIV in HIV-positive and HIV-negative patients with respiratory infections in hospitals in South Africa and determine their genotypes.

STUDY DESIGN

Specimens from patients with acute respiratory infections from hospitals serving Pretoria were screened for WUV and KIV. Positive specimens were sequenced and subjected to phylogenetic analysis.

RESULTS

WUV was identified in (7%) and KIV in (1%) of mainly pediatric patients. Co-infections were common in WUV- and KIV-infected patients (71% and 66.6%, respectively); 57% of patients with WUV and 33% of patients with KIV were HIV-positive while the HIV prevalence in the respiratory virus patient group screened in this study was 33% WUV and KIV patients presented with moderate to severe lower respiratory tract disease. Four distinct and 2 unique WUV strains were identified clustering into 2 of 4 globally identified genotypes. KIV strains were identical to strains from Sweden.

CONCLUSION

WUV is frequently detected in HIV-infected patients with respiratory disease, but its role as respiratory pathogen remains uncertain.

Merkel cell carcinoma

Merkel cell carcinoma (MCC) is a highly aggressive neuroendocrine carcinoma of the skin. More than one-third of MCC patients will die from this cancer, making it twice as lethal as malignant melanoma. Despite the fact that MCC is still a very rare tumor, its incidence is rapidly increasing; the American Cancer Society estimates for 2008 almost 1,500 new cases in the USA. These clinical observations are especially disturbing as the pathogenesis of MCC is not yet fully understood; however, a number of recent reports contribute to a better understanding of its pathogenesis. Here we describe findings regarding the role of Wnt, MAPK and Akt signaling as well as possible aberrations in the p14ARF/p53/RB tumor suppressor network in MCC. Most important, and possibly with high impact on future therapeutic approaches is the demonstration that a polyomavirus has frequently integrated in the genome of the MCC cells prior to tumor development.

A single-tube, real-time PCR assay for detection of the two newly characterized human KI and WU polyomaviruses

BACKGROUND

Three new human polyomaviruses have been recently described, and investigating their in vivo biology and pathogenicity will require sensitive and rational detection assays.

OBJECTIVES

To develop and evaluate a sensitive and rational assay for detection of the newly identified KI and WU polyomaviruses.

STUDY DESIGN

A single-tube, dual-probe, real-time PCR assay for simultaneous detection and discrimination of KI and WU polyomaviruses was developed.

RESULTS

The assay had near single-molecule sensitivity for both viruses and no cross-reactivity was observed. A panel of 637 nasopharyngeal aspirates was screened, resulting in a frequency of 1.4% for KIPyV and 1.3% for WUPyV.

CONCLUSIONS

The dual-probe assay provides a rational approach for further studies of KIPyV and WUPyV.

KI and WU polyomaviruses in children, France

KI and WU Polyomaviruses in Children, France

[The correlation between the polyomavirus DNA load and the dose of immunosuppressant]

OBJECTIVE

To explore the correlation between the polyomavirus DNA load and the dose of immunosuppressant in patients with allogene bone marrow transplantation (allo-BMT) for preventing the development of post-transplantational hemorrhagic cystitis.

METHODS

Serial blood and urine samples from 122 cases of allo-BMT recipients were obtained and DNA was extracted from urine samples. Polyomavirus DNA-specific probe was synthesized and Fluorescence quantitative polymerase chain reaction was used for detecting the polyomavirus DNA loads and Fluorescence polarization immunoassay (FPIA) was performed for determining the dose of immunosuppressant Cyclosporin A (CsA) in blood.

RESULTS

The altered polyomavirus DNA load in urine was followed by concentration of CsA in blood. When the concentration of CsA in blood was higher than 86-105 ng/ml, the positive rate of polyomavirus DNA load was significantly increased and both presented the linable correlation.

CONCLUSION

In immunosuppression condition, polyomavirus DNA load correlated to the dose of immunosuppressant, which increased the risk of post-transplantational hemorrhagic cystitis.

[Identification of KI polyomavirus in children with lower respiratory tract infections from Zhejiang region of China]

KI polyomavirus, which was firstly discovered in 2007, is a new human polyomavirus belonging to Polyomaviridae and containing circular double-strand genomic DNA. This study was based on identification assay of KI polyomavirus reported. Total 2293 clinical sputum specimens from children under 3-years-old were collected and screened from Wenzhou Medical College affiliated Wenling Hospital, Zhejiang Province. A KI polyomavirus was detected and identified, the positive rate was 0.04%. The sequences of PCR products was identical to that of the viral capsid protein (VP1) gene derived from KI polyomavirus. The results strongly suggested that the KI polyomavirus was found firstly in Chinese children with acute lower respiratory tract infections from Zhejiang region. This study provided new information for further investigation of etiopathogenisis and diagnosis in children with lower respiratory tract infections.

Age-related pattern of KI and WU polyomavirus infection

Background

The role of two recently identified polyomaviruses, KI and WU, in the causation of respiratory disease has not been established.

Objectives

To determine the prevalence of KI and WU viruses (KIV and WUV) in 371 respiratory samples and evaluate their contribution to respiratory disease.

Study Design

Specimens were screened for KIV and WUV using single, multiplex or real time PCR; co-infection with other respiratory viruses was evaluated.

Results

Of the 371 samples analysed, 10 (2.70%) were positive for KIV and 4 (1.08%) were positive for WUV yielding an overall case prevalence of KIV and WUV infection of 3.77%. KIV and WUV were identified in patients aged <15 years (11 patients) with upper or lower respiratory tract infection and >45 years (3 patients) with upper respiratory tract infection. Co-infections were found in 5 (50%) and 3 (75%) of the KIV and WUV positive samples, respectively.

Conclusions

This study supports previous conclusions that KIV and WUV detection in the respiratory tract may be coincidental and reflect reactivation of latent or persistent infection with these viruses. The age distribution of KIV and WUV infection in this study mirrors that found for the other human polyomaviruses, BK and JC.

Receptor-binding and oncogenic properties of polyoma viruses isolated from feral mice

Laboratory strains of the mouse polyoma virus differ markedly in their abilities to replicate and induce tumors in newborn mice. Major determinants of pathogenicity lie in the sialic binding pocket of the major capsid protein Vp1 and dictate receptor-binding properties of the virus. Substitutions at two sites in Vp1 define three prototype strains, which vary greatly in pathogenicity. These strains replicate in a limited fashion and induce few or no tumors, cause a disseminated infection leading to the development of multiple solid tumors, or replicate and spread acutely causing early death. This investigation was undertaken to determine the Vp1 type(s) of new virus isolates from naturally infected mice. Compared with laboratory strains, truly wild-type viruses are constrained with respect to their selectivity and avidity of binding to cell receptors. Fifteen of 15 new isolates carried the Vp1 type identical to that of highly tumorigenic laboratory strains. Upon injection into newborn laboratory mice, the new isolates induced a broad spectrum of tumors, including ones of epithelial as well as mesenchymal origin. Though invariant in their Vp1 coding sequences, these isolates showed considerable variation in their regulatory sequences. The common Vp1 type has two essential features: 1) failure to recognize “pseudoreceptors” with branched chain sialic acids binding to which would attenuate virus spread, and 2) maintenance of a hydrophobic contact with true receptors bearing a single sialic acid, which retards virus spread and avoids acute and potentially lethal infection of the host. Conservation of these receptor-binding properties under natural selection preserves the oncogenic potential of the virus. These findings emphasize the importance of immune protection of neonates under conditions of natural transmission.

Strains of the mouse polyoma virus adapted to growth in cell culture vary greatly in their abilities to cause disease. Pathogenicities of these laboratory strains range from “attenuated” to “highly virulent” when tested in animals. The biological differences are based in large part on variations in the outer capsid protein, which dictate the manner in which the virus recognizes and binds to cell receptors. In contrast, strains of virus newly isolated from wild mice are uniform in their receptor-binding properties. Naturally occurring strains avoid binding to pseudoreceptors, which would severely limit their ability to spread. At the same time, their avidity of binding to true receptors is sufficiently strong to avoid rapid dissociation and potentially lethal spread. They are therefore neither attenuated nor virulent. The new isolates do, however, retain the ability to induce a broad spectrum of tumors in the laboratory. These findings emphasize the importance of neonatal and maternal immune responses in allowing a potentially highly oncogenic virus to disseminate without causing disease.

Detection of oncogenic DNA viruses in colorectal cancer

BACKGROUND

As a part of our search for oncogenic viruses as potential etiological agents in human malignancies, our studies on human papillomaviruses (HPV) were extended to analysis of the 3 polyomaviruses (SV40, BKV and JCV) in colorectal carcinomas.

PATIENTS AND METHODS

Archival tumour samples from 71 patients with colorectal cancer were analyzed for the sequences of SV40, BKV, JCV and HPV using PCR-based techniques. HPV genotypes were determined using sequencing and reverse blot hybridization (InnoLipa).

RESULTS

Amplification of BKV and JCV with the primer pair PEP-1 and PEP-2 and subsequent restriction digestion of the amplified products with BamH I disclosed BKV in 6/66 (9%) of the samples, whereas none contained JCV. SV40 was amplified in 10/66 (15.1%) samples and confirmed by sequencing analysis. In pair-wise analysis for co-infections, the samples were significantly different in their BKV-JCV and JCV-SV40 status, in contrast to their BKV-SV40 co-infection status. HPV DNA was detected in 22/66 (33.3%) of the samples analysed with either the MY09/11 or SPF primer mix. Of these 22 HPV infections, 7 were single-type infections and 15 contained multiple HPV types. HPV detection or type distribution showed no relationship to the gender of the patients or histological grade of the tumour. HPV status was not significantly related to detection of BKV, JCV or SV40. Similarly, in pair-wise analysis for co-infections, the samples were significantly different in their status of HPV-BKV (p=0.0006), HPV-JCV (p=0.0001), and HPV-SV40 (p=0.019), implicating that HPV and the 3 polyomaviruses are rarely detected concomitantly in the same samples.

CONCLUSION

Taking the known molecular mechanisms of action of these individual viruses, there is a chance that these viruses could alter the mechanisms of cell cycle control and inhibit apoptosis, thus potentially causing chromosomal instability and promoting colorectal oncogenesis.

Clonal integration of a polyomavirus in human Merkel cell carcinoma

Merkel cell carcinoma (MCC) is a rare but aggressive human skin cancer that typically affects elderly and immunosuppressed individuals, a feature suggestive of an infectious origin. We studied MCC samples by digital transcriptome subtraction and detected a fusion transcript between a previously undescribed virus T antigen and a human receptor tyrosine phosphatase. Further investigation led to identification and sequence analysis of the 5387-base-pair genome of a previously unknown polyomavirus that we call Merkel cell polyomavirus (MCV or MCPyV). MCV sequences were detected in 8 of 10 (80%) MCC tumors but only 5 of 59 (8%) control tissues from various body sites and 4 of 25 (16%) control skin tissues. In six of eight MCV-positive MCCs, viral DNA was integrated within the tumor genome in a clonal pattern, suggesting that MCV infection and integration preceded clonal expansion of the tumor cells. Thus, MCV may be a contributing factor in the pathogenesis of MCC.

Polyomaviruses of nonhuman primates: implications for research

Polyomaviruses are a family of small nonenveloped DNA viruses that infect birds and mammals. At least 7 nonhuman primate polyomaviruses that occur in macaques, African green monkeys, marmosets baboons, and chimpanzees have been described, as well as 4 polyomaviruses that occur in humans. Simian virus 40 (SV40), which infects macaques, was the first nonhuman primate polyomavirus identified as a contaminant of early polio vaccines. Primate polyomaviruses cause inapparent primary infections but persist in the host and can cause severe disease in situations of immunocompromise. This review describes the primate polyomaviruses, and the diseases associated with the viruses of macaques. In macaques, the greatest current concerns are the potential confounding of study results by polyomavirus infections and the zoonotic potential of SV40.

[WU polyomavirus and KI polyomavirus detected in specimens from children with acute respiratory tract infection in China]

OBJECTIVE

To investigate newly identified polyomavirus WUV and WUV and KIPyV are associated with acute respiratory infections in China, tests were developed to detect WUV and KIPyV gene fragments from nasopharyngeal aspirates collected from children with ARI fron Nov. 2006 to Oct. 2007.

METHODS

A total of 318 clinical samples were tested for WUV and KIPyV using PCR method. The positive products were sequenced and compared with those in GenBank.

RESULTS

14 of the 318 Samples were positive (WUV was 2.2%, KIPyV was 2.2%). All of children who were positive for WUV or KIPyV had respiratory illness.

CONCLUSION

Polyomavirus WU and KIPyV infection may be associated with upper and lower respiratory diseases.

[Discovery and identification of WU polyomavirus in children from Zhejing region]

WU polyomavirus, which was firstly discovered in 2007, is a new human polyomavirus belonging to Polyomaviridae and containing circular double-stranded genomic DNA. In this study, the 278 clinical sputum specimens from children under 5 years old were collected from Wenzhou Medical College affiliated Wenling First Hospital, Zhejiang Province. Based on identification assay of WU polyomavirus previously reported, a WU polyomavirus was identified from clinical samples successfully, the positive rate was 0.4%. The sequences of PCR products were identical to that of VP2 gene and large T antigen gene derived from WU polyomavirus reported. The above results strongly suggested that the WU polyomavirus isolated was firstly found in Chinese children with acute lower respiratory tract infections. This study provides a firm basis for further research of WU polyomavirus.

Infectious offspring: how birds acquire and transmit an avian polyomavirus in the wild

Detailed patterns of primary virus acquisition and subsequent dispersal in wild vertebrate populations are virtually absent. We show that nestlings of a songbird acquire polyomavirus infections from larval blowflies, common nest ectoparasites of cavity-nesting birds, while breeding adults acquire and renew the same viral infections via cloacal shedding from their offspring. Infections by these DNA viruses, known potential pathogens producing disease in some bird species, therefore follow an 'upwards vertical' route of an environmental nature mimicking horizontal transmission within families, as evidenced by patterns of viral infection in adults and young of experimental, cross-fostered offspring. This previously undescribed route of viral transmission from ectoparasites to offspring to parent hosts may be a common mechanism of virus dispersal in many taxa that display parental care.

Development and evaluation of real-time PCR assays for the detection of the newly identified KI and WU polyomaviruses

Background

Recently, novel human polyomaviruses, KI (KIV) and WU (WUV) were described. Their role in human disease has not yet been determined.

Objectives

The aim of this study was to develop sensitive and specific assays for the detection of KIV and WUV.

Study

Two KIV (KI-A and KI-B) and three WUV (WU-A, WU-B and WU-C) real-time polymerase chain reaction (rtPCR) assays were developed and evaluated. Clinical sensitivities and specificities were determined by testing 200 respiratory specimens and the results compared to those for previously described conventional PCR assays. Limits of detection were determined, and the analytical specificities of the assays were investigated.

Results

No cross-reactivity was observed between the rtPCR methods and unrelated organisms. All five rtPCR assays could reliably detect 10 copies of genomic DNA equivalents per reaction, which was more sensitive than conventional methods. Compared to the conventional PCR assays, the sensitivity of the KI-A, KI-B, WU-A, WU-B and WU-C assays was 100%, 86.7% 95.5%, 100% and 100%, respectively. Specificity was 94.6%, 97.3%, 96.6%, 97.7% and 97.2%, respectively.

Conclusions

The KI-A, WU-B and WU-C assays provide the most sensitive detection of KIV and WUV in clinical specimens and may be used for further research into these viruses.

A newly reported human polyomavirus, KI virus, is present in the respiratory tract of Australian children

Background

Recently, Allander and co-workers reported the discovery of a new human polyomavirus, KI virus, in respiratory secretions from patients with acute respiratory tract infection (ARTI).

Objective

We examined 951 respiratory samples collected in Queensland, Australia, between November 2002 and August 2003 from patients with respiratory infection, for the presence of the KI virus.

Results

Twenty-four (2.5%) samples were positive for KI virus with 20 (83%) of these from children younger than 5 years. In six (25%) patients KI was co-detected with another virus. Full genome sequencing of three isolates shows a high degree of conservation between the Queensland isolates and the original isolates reported from Swedish patients.

Conclusions

The newly described KI polyomavirus may commonly be found in the respiratory tract of patients with ARTI, particularly children, and results indicate that the virus has global presence.

Detection of polyomaviruses and herpesviruses in human adrenal tumors

The presence of polyomaviruses and herpesviruses in adrenal tumors and their role in adrenal tumorigenesis has never been investigated, even though the adrenal gland seems to be a preferential site of infection by these viruses and adrenal steroid hormones have been shown to activate their replication. We examined in a large series of normal adrenal gland tissues (n=20) and adrenal tumors (n=107) the presence of herpesviruses and polyomaviruses sequences and gene expression, which were detected in a high proportion of both normal and neoplastic adrenal samples (overall, viruses were found in 15% normal adrenals, 27.8% benign adrenal tumors and 35.3% malignant tumors). The polyomaviruses SV40 and BK virus were more frequently found in malignant adrenal tumors, whereas herpesviruses, especially Epstein-Barr virus and human cytomegalovirus, were more frequently detected in functioning benign adrenocortical tumors, often as coinfection. Moreover, tumors from patients with severe hypercortisolism frequently showed herpesvirus coinfections at high viral genome copy number. Our study suggests that the adrenal gland could be a reservoir of infection for these viruses and that hormone overproduction by the adrenal gland could represent a trigger for virus reactivation. On the other hand, these viruses could also contribute to adrenal cell proliferation and tumorigenesis.

Urine cytology findings of polyomavirus infections

Polyomaviruses of the BK- and JC-strains often remain latent within the transitional cell layer of the bladder, ureters and the renal pelvis as well as in tubular epithelial cells of the kidney. Slight changes in the immune status and/or an immunocompromised condition can lead to the (re)activation of latent polyomaviruses, especially along the transitional cell layer, resulting in the shedding of viral particles and infected cells into the urine. A morphologic sign of the (re)activation of polyomaviruses is the detection of typical intranuclear viral inclusion bearing epithelial cells, so-called "decoy cells", in the urine. Decoy cells often contain polyoma-BK-viruses. The inclusion bearing cells are easily identified and quantifiable in routine Papanicolaou stained urine cytology specimens. With some experience, decoy cells can also be detected in the unstained urinary sediment by phase contrast microscopy. Different morphologic variants of decoy cells (types 1 through 4) are described and ancillary techniques (immunohistochemistry, electron microscopy (EM), and fluorescence-in-situ-hybridization (FISH)) for proper identification and characterization are discussed. Special emphasis is placed on the clinical significance of the detection of decoy cells as a parameter to assess the risk for disease, i.e., polyoma-BK-virus nephropathy (BKN) in kidney transplant recipients. The sensitivity and specificity of decoy cells for diagnosing BKN is 99% and 95%, respectively, the positive predictive value varies between 27% and more than 90%, and the negative predictive value is 99%. The detection of decoy cells is compared to other techniques applicable to assess the activation of polyomaviruses in the urine (polymerase chain reaction (PCR) and EM).

Identification of a novel polyomavirus from patients with acute respiratory tract infections

We report the identification of a novel polyomavirus present in respiratory secretions from human patients with symptoms of acute respiratory tract infection. The virus was initially detected in a nasopharyngeal aspirate from a 3-year-old child from Australia diagnosed with pneumonia. A random library was generated from nucleic acids extracted from the nasopharyngeal aspirate and analyzed by high throughput DNA sequencing. Multiple DNA fragments were cloned that possessed limited homology to known polyomaviruses. We subsequently sequenced the entire virus genome of 5,229 bp, henceforth referred to as WU virus, and found it to have genomic features characteristic of the family Polyomaviridae. The genome was predicted to encode small T antigen, large T antigen, and three capsid proteins: VP1, VP2, and VP3. Phylogenetic analysis clearly revealed that the WU virus was divergent from all known polyomaviruses. Screening of 2,135 patients with acute respiratory tract infections in Brisbane, Queensland, Australia, and St. Louis, Missouri, United States, using WU virus–specific PCR primers resulted in the detection of 43 additional specimens that contained WU virus. The presence of multiple instances of the virus in two continents suggests that this virus is geographically widespread in the human population and raises the possibility that the WU virus may be a human pathogen.

We have identified a novel virus, referred to as WU virus, in the family Polyomaviridae by screening of human respiratory secretions. Two human polyomaviruses, BK and JC, were identified in 1971 and infect the majority of humans around the world. These two viruses are closely related to each other and are both are pathogenic in immunocompromised individuals. Earlier this year, a third polyomavirus, KI, was described in human clinical specimens, although its pathogenicity and prevalence in humans has not yet been established. The discovery of WU virus brings the number of polyomaviruses detected in humans to four. WU differs from BK and JC significantly in its genome sequence and in its relative tissue tropism, suggesting that it is likely to have unique biological properties. This discovery raises many questions for further investigation, such as, Is WU virus a human pathogen? If so, what kind of disease does it cause? Where in the body does WU virus reside? At what age does infection typically occur? Perhaps most importantly, there are likely to be many more as of yet unidentified viruses infecting the human body.