Novel human polyomaviruses in pregnancy: higher prevalence of BKPyV, but no WUPyV, KIPyV and HPyV9

KI and WU Polyomaviruses: Seroprevalence Study and DNA Prevalence in SARS-CoV-2 RNA Positive and Negative Respiratory Samples

The aim of this work was to study the possible co-infection of KI and WU polyomavirus (KIPyV and WUPyV, respectively) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in respiratory samples and to detect the seroprevalence of KIPyV and WUPyV. A total of 1030 nasopharyngeal samples were analyzed from SARS-CoV-2 RNA positive (n = 680) and negative (n = 350) adults and children (age: 1 day to 94.2 years) collected from August 2020 to October 2021. KIPyV DNA was detected in two SARS-CoV-2-positive samples (2/680, 0.29%) and in three SARS-CoV-2-negative samples (3/350, 0.86%). WUPyV DNA was observed in one-one samples from both groups (1/680, 0.15% vs. 1/350, 0.29%). We did not find an association between SARS-CoV-2 and KIPyV or WUPyV infection, and we found low DNA prevalence of polyomaviruses studied after a long-term lockdown in Hungary. To exclude a geographically different distribution of these polyomaviruses, we studied the seroprevalence of KIPyV and WUPyV by enzyme-linked immunosorbent assay among children and adults (n = 692 for KIPyV and n = 705 for WUPyV). Our data confirmed that primary infections by KIPyV and WUPyV occur mainly during childhood; the overall seropositivity of adults was 93.7% and 89.2% for KIPyV and WUPyV, respectively. Based on our data, we suggest that the spread of KIPyV and WUPyV might have been restricted in Hungary by the lockdown.

HPyV6 and HPyV7 in urine from immunocompromised patients

Background

Human polyomavirus 6 (HPyV6) and HPyV7 are two of the novel polyomaviruses that were originally detected in non-diseased skin. Serological studies have shown that these viruses are ubiquitous in the healthy adult population with seroprevalence up to 88% for HPyV6 and 72% for HPyV7. Both viruses are associated with pruritic skin eruption in immunocompromised patients, but a role with other diseases in immunoincompetent patients or malignancies has not been established.

Methods

PCR was used to determine the presence of HPyV6 and HPyV7 DNA in urine samples from systemic lupus erythematosus (n = 73), multiple sclerosis (n = 50), psoriasis vulgaris (n = 15), arthritic psoriasis (n = 15) and HIV-positive patients (n = 66). In addition, urine from pregnant women (n = 47) and healthy blood donors (n = 20) was investigated.

Results

HPyV6 DNA was detected in 21 (28.8%) of the urine specimens from SLE patients, in 6 (9.1%) of the urine samples from the HIV-positive cohort, and in 19 (40.4%) samples from pregnant women. HPyV7 DNA was only found in 6 (8.2%) of the urine specimens from SLE patients and in 4 (8.5%) samples from pregnant women. No HPyV6 and HPyV7 viruria was detected in the urine samples from the other patients.

Conclusions

HPyV6, and to a lesser extend HPyV7, viruria seems to be common in SLE and HIV-positive patients, and pregnant women. Whether these viruses are of clinical relevance in these patients is not known.

Beyond Cytomegalovirus and Epstein-Barr Virus: a Review of Viruses Composing the Blood Virome of Solid Organ Transplant and Hematopoietic Stem Cell Transplant Recipients

Viral primary infections and reactivations are common complications in patients after solid organ transplantation (SOT) and hematopoietic stem cell transplantation (HSCT) and are associated with high morbidity and mortality. Among these patients, viral infections are frequently associated with viremia. Beyond the usual well-known viruses that are part of the routine clinical management of transplant recipients, numerous other viral signatures or genomes can be identified in the blood of these patients. The identification of novel viral species and variants by metagenomic next-generation sequencing has opened up a new field of investigation and new paradigms. Thus, there is a need to thoroughly describe the state of knowledge in this field with a review of all viral infections that should be scrutinized in high-risk populations. Here, we review the eukaryotic DNA and RNA viruses identified in blood, plasma, or serum samples of pediatric and adult SOT/HSCT recipients and the prevalence of their detection, with a particular focus on recently identified viruses and those for which their potential association with disease remains to be investigated, such as members of the Polyomaviridae, Anelloviridae, Flaviviridae, and Astroviridae families. Current knowledge of the clinical significance of these viral infections with associated viremia among transplant recipients is also discussed. To ensure a comprehensive description in these two populations, individuals described as healthy (mostly blood donors) are considered for comparative purposes. The list of viruses that should be on the clinicians' radar is certainly incomplete and will expand, but the challenge is to identify those of possible clinical significance.

A Role of Sp1 Binding Motifs in Basal and Large T-Antigen-Induced Promoter Activities of Human Polyomavirus HPyV9 and Its Variant UF-1

Human polyomavirus 9 (HPyV9) was originally detected in the serum of a renal transplant patient. Seroepidemiological studies showed that ~20-50% of the human population have antibodies against this virus. HPyV9 has not yet been associated with any disease and little is known about the route of infection, transmission, host cell tropism, and genomic variability in circulating strains. Recently, the HPyV9 variant UF-1 with an eight base-pair deletion, a thirteen base-pair insertion and with point mutations, creating three putative Sp1 binding sites in the late promoter was isolated from an AIDS patient. Transient transfection studies with a luciferase reporter plasmid driven by HPyV9 or UF1 promoter demonstrated that UF1 early and late promoters were stronger than HPyV9 promoters in most cell lines, and that the UF1 late promoter was more potently activated by HPyV9 large T-antigen (LTAg). Mutation of two Sp1 motifs strongly reduced trans-activation of the late UF1 promoter by HPyV9 LTAg in HeLa cells. In conclusion, the mutations in the UF1 late promoter seem to strengthen its activity and its response to stimulation by HPyV9 LTAg in certain cells. It remains to be investigated whether these promoter changes have an influence on virus replication and affect the possible pathogenic properties of the virus.

First detection and complete genome sequence of a phylogenetically distinct human polyomavirus 6 highly prevalent in human bile samples

Oncovirus-associated malignancies are potentially preventable diseases with major public health significance. Human polyomaviruses (HPyVs) may be associated with oncogenesis or symptomatic illnesses in immunocompromised patients, but the site of viral shedding of most recently discovered HPyVs remains obscure. Using real-time PCR assay using specific primers targeting the HPyV6 large tumor antigen gene, we detected a phylogenetically distinct HPyV6 which was highly prevalent in the bile samples of patients with malignant biliary obstruction (18.8%) and acute gallstone cholangitis (5.5%). The prevalence rate and mean viral load of this HPyV6 were highest in the cholangiocarcinoma subgroup (27.6% and 2.41 × 10⁴copies/ml). These findings were confirmed with another real-time PCR assay using specific primers targeting the HPyV6 viral capsid protein 2 gene. These bile HPyV6 strains may represent a novel clade of HPyV6 as they formed a distinct cluster from the other HPyV6s and exhibited >2% differences in amino acid sequences in their major proteins. While HPyV6 was unlikely the cause of the patients' acute symptoms and liver dysfunction, the virus may be related to immunosuppression in patients with malignancy and/or important in the oncogenesis of cholangiocarcinoma in patients without coinfection with other oncogenic microbes. Further studies to ascertain a causative role of HPyV6 in cholangiocarcinoma should be conducted.

No Evidence of Human Polyomavirus 9, WU and KI DNA in Kidney and Urinary Bladder Tumour Tissue Samples

BACKGROUND/AIMS

The oncogenic potential of human polyomaviruses (HPyVs) has been proposed, but so far only Merkel cell carcinoma polyomavirus seems to be associated with a human tumour. The role of BK polyomavirus (BKPyV) in human tumourigenesis remains controversial. BKPyV establishes persistent infection in the urinary tract, and renal and bladder neoplasms have been studied extensively, but conflicting prevalence data are reported. KI, WU and HPyV9 were detected in urine samples suggesting that these viruses may also infect the urinary tract, but their presence in urinary tract tumours has not been studied. The aim of this work was to examine the prevalence of KIPyV, WUPyV, HPyV9 and BKPyV by PCR in renal and bladder neoplasms.

METHODS

A total of 190 formalin-fixed paraffin-embedded renal neoplasms, bladder cancer and kidney biopsy samples were analysed for the presence of BKPyV, KIPyV, WUPyV and HPyV9 DNA by real-time and nested PCR.

RESULTS

Amplifiable DNA was extracted from all the samples, but none of the studied viruses were detected in benign renal neoplasia (0/23), malignant renal tumours (0/89) or bladder cancer (0/76).

CONCLUSION

Our study did not find any evidence that BKPyV, KIPyV, WUPyV or HPyV9 are associated with bladder and renal tumours.

Characterization of the non-coding control region of polyomavirus KI isolated from nasopharyngeal samples from patients with respiratory symptoms or infection and from blood from healthy blood donors in Norway

Seroepidemiological studies showed that the human polyomavirus KI (KIPyV) is common in the human population, with age-specific seroprevalence ranging from 40-90 %. Genome epidemiological analyses demonstrated that KIPyV DNA is predominantly found in respiratory tract samples of immunocompromised individuals and children suffering from respiratory diseases, but viral sequences have also been detected in brain, tonsil, lymphoid tissue studies, plasma, blood and faeces. Little is known about the sequence variation in the non-coding control region of KIPyV variants residing in different sites of the human body and whether specific strains dominate in certain parts of the world. In this study, we sequenced the non-coding control region (NCCR) of naturally occurring KIPyV variants in nasopharyngeal samples from patients with respiratory symptoms or infection and in blood from healthy donors in Norway. In total 86 sequences were obtained, 44 of which were identical to the original isolated Stockholm 60 variant. The remaining NCCRs contained one or several mutations, none of them previously reported. The same mutations were detected in NCCRs amplified from blood and nasopharyngeal samples. Some patients had different variants in their specimens. Transient transfection studies in HEK293 cells with a luciferase reporter plasmid demonstrated that some single mutations had a significant effect on the relative early and late promoter strength compared with the Stockholm 60 promoter. The effect of the NCCR mutations on viral replication and possible virulence properties remains to be established.

Significance, cytomorphology of decoy cells in polyomavirus-associated nephropathy: Review of clinical, histopathological, and virological correlates with commentary

Human polyomaviruses (PyV) are ubiquitous, remaining predominantly inactive hence asymptomatic in the healthy, immunocompetent population. BK and JC PyV potentially infect pan-urinary tract epithelial cells. With reactivation, PyV disrupt cell cycling mechanisms, facilitating viral replication leading to cell necrosis, exfoliation, and, infrequently, carcinogenesis. Exfoliated PyV-infected cells pose diagnostic pitfalls, hence they are termed "decoy cells" as they may mimic high-grade urothelial carcinoma cells. BK polyomavirus-associated-nephropathy (BKVAN) is an inflammatory disease causing interstitial fibrosis with tubular atrophy in renal transplant recipients, increasing risk of graft loss. BKVAN is confirmed by renal biopsy, and managed by immunosuppression modulation. As voided urine may provide pan-reno-urinary tract sampling, cytopathology may serve a critical diagnostic purpose coupled with decoy cell quantification and indirect BK PyV load gauging. Thus, identification of decoy cells and differentiation from high-grade urothelial carcinoma cells, and degenerated, benign urothelial cells, is clinically essential. PyV virology and pathobiology in the context of renal transplantation, immuno-suppression and BKVAN, and, decoy cell cytomorphology and cytopreparation with commentary are highlighted. Decoy cell overall characteristics: variable degeneration; cytomegaly; comet-like shapes; angular cytoplasmic extensions; eccentric, polar nuclear placements; moderate anisocytosis; typically single cells with high N:C ratios. Cytoplasmic features: moderate-abundance; granular, blue-gray monochromatism. Nuclear features: karyomegaly; haphazardly-scattered chromatin densities; smudged, homogeneous, basophilic ground glass masses displacing chromatin alongside inner periphery of regular, symmetrical nuclear envelopes. Background features: granular cellular debris; inflammatory cells; intact and lyzed erythrocytes. Decoy cells lack coarse chromatin as in high-grade urothelial carcinoma cells. Benign urothelial cells exhibit low N:C ratios with fine chromatin distribution and euchromasia.

Early and late promoters of BK polyomavirus, Merkel cell polyomavirus, Trichodysplasia spinulosa-associated polyomavirus and human polyomavirus 12 are among the strongest of all known human polyomaviruses in 10 different cell lines

Recently, 11 new human polyomaviruses (HPyVs) have been isolated and named KI, WU, Merkel cell polyomavirus (MCPyV), HPyV6,  -7,  -9,  -10 and  -12, Trichodysplasia spinulosa-associated polyomavirus (TSPyV), STLPyV and NJPyV-2013. Little is known about cell tropism of the novel HPyVs, and cell cultures allowing virus propagation are lacking. Because viral tropism partially depends on the interaction of cellular transcription factors with the viral promoter, we monitored the promoter activity of all known HPyVs. Therefore, we compared the relative early and late promoter activity of the BK polyomavirus (BKPyV) (WW strain) with the corresponding activities of the other HPyVs in 10 different cell lines derived from brain, colon, kidney, liver, lung, the oral cavity and skin. Our results show that the BKPyV, MCPyV, TSPyV and HPyV12 early promoters displayed the strongest activity in most cell lines tested, while the remaining HPyV had relative low early promoter activity. HPyV12 showed the highest late promoter activity of all HPyVs in most cell lines, but also the BKPyV, MCPyV and TSPyV late promoters belonged to the stronger ones among HPyVs. The HPyVs with weak early promoter activity had in general also weak late promoter activity, except for HPyV10 whose late promoter was relatively strong in six of the 10 cell lines. A 20 bp deletion in the promoter of an HPyV12 variant significantly affected both early and late promoter activity in most cell lines. In conclusion, our findings suggest which cell lines may be suitable for virus propagation and may give an indication of the cell tropism of the HPyVs.

A rolling circle amplification screen for polyomaviruses other than BKPyV in renal transplant recipients confirms high prevalence of urinary JCPyV shedding

OBJECTIVES

Multiple novel human polyomaviruses (HPyVs) have been discovered in the last few years. These or other, unknown, nephrotropic HPyVs may potentially be shed in urine.

METHODS

To search for known and unknown HPyVs we investigated BKPyV-negative urine samples from 105 renal transplant recipients (RTR) by rolling circle amplification (RCA) analysis and quantitative JCPyV PCR. Clinical data was analysed to identify risk factors for urinary polyomavirus shedding.

RESULTS

In 10% (11/105) of the urine samples RCA with subsequent sequencing revealed JCPyV, but no other HPyV sequences. Using quantitative JCPyV PCR, 24% (25/105) of the samples tested positive. Overall sensitivities of RCA of 44% (11/25) in detecting JCPyV in JCPyV DNA-positive urine and 67% (10/15) for samples with JCPyV loads >10,000 copies/ml can be assumed. Despite frequent detectable urinary shedding of JCPyV in our cohort, this could not be correlated with clinical risk factors.

CONCLUSION

Routine urinary JCPyV monitoring in BKPyV-negative RTR without suspected polyomavirus-associated nephropathy might be of limited diagnostic value. As RCA works in a sequence-independent manner, detection of novel and known polyomaviruses shed in sufficient quantities is feasible. High-level shedding of HPyVs other than BKPyV or JCPyV in the urine of RTR is unlikely to occur.

Human polyomavirus 9 infection in kidney transplant patients

This virus is frequently found within the first year after transplantation and in association with BK polyomavirus infection.

Several human polyomaviruses of unknown prevalence and pathogenicity have been identified, including human polyomavirus 9 (HPyV9). To determine rates of HPyV9 infection among immunosuppressed patients, we screened serum samples from 101 kidney transplant patients in the Netherlands for HPyV9 DNA and seroreactivity. A total of 21 patients had positive results for HPyV9 DNA; positivity rates peaked at 3 months after transplantation, but the highest viral loads were measured just after transplantation. During 18 months of follow-up, HPyV9 seroprevalence increased from 33% to 46% among transplant patients; seroprevalence remained stable at ≈30% in a control group of healthy blood donors in whom no HPyV9 DNA was detected. Further analysis revealed an association between detection of HPyV9 and detection of BK polyomavirus but not of cytomegalovirus. Our data indicate that HPyV9 infection is frequent in kidney transplant patients, but the nature of infection—endogenous or donor-derived—and pathogenic potential of this virus remain unknown.

WU and KI polyomaviruses in respiratory, blood and urine samples from renal transplant patients

BACKGROUND

It is suggested that immunosuppression due to transplantation might be a risk for human polyomavirus KI (KIPyV) and WU (WUPyV) infection. Most of the publications report data about stem cell transplant patients, little is known about these virus infections in renal transplant patients.

OBJECTIVES

To study the presence of KIPyV and WUPyV in upper respiratory, plasma and urine samples from renal transplant patients. To analyse clinical and personal data.

STUDY DESIGN

532 respiratory, 503 plasma and 464 urine samples were collected from 77 renal transplant patients. KIPyV and WUPyV were detected by nested and quantitative real-time PCR. Patient and clinical data from medical records were analyzed.

RESULTS

KIPyV was detected in respiratory, plasma and urine samples from 14.3%, 3.9% and 4.1% of renal transplant patients. WUPyV was found in respiratory and plasma specimens from 9.1% and 5.3% of the patients. Significant association was revealed between the detection of KIPyV and WUPyV and the time of samples collection and the age of the patients. KIPyV was presented in respiratory and plasma sample at the same time. KIPyV was detected in plasma samples from two patients and in urine samples of three other patients providing also KIPyV positive respiratory samples at the same time. No clinical consequences of KIPyV or WUPyV infection were found.

CONCLUSION

Although no clinical consequences of KIPyV and WUPyV infections were found in renal transplant patients, it is suggested that renal transplantation might result in higher susceptibility or reactivation of these infection.

Neutralizing and IgG antibodies against simian virus 40 in healthy pregnant women in Italy

OBJECTIVE

Polyomavirus simian virus 40 (SV40) sequences have been detected in various human specimens and SV40 antibodies have been found in human sera from both healthy individuals and cancer patients. This study analyzed serum samples from healthy pregnant women as well as cord blood samples to determine the prevalence of SV40 antibodies in pregnancy.

METHODS

Serum samples were collected at the time of delivery from two groups of pregnant women as well as cord bloods from one group. The women were born between 1967 and 1993. Samples were assayed by two different serological methods, one group by neutralization of viral infectivity and the other by indirect ELISA employing specific SV40 mimotopes as antigens. Viral DNA assays by real-time polymerase chain reaction were carried out on blood samples.

RESULTS

Neutralization and ELISA tests indicated that the pregnant women were SV40 antibody-positive with overall prevalences of 10.6% (13/123) and 12.7% (14/110), respectively. SV40 neutralizing antibodies were detected in a low number of cord blood samples. Antibody titers were generally low. No viral DNA was detected in either maternal or cord bloods.

CONCLUSIONS

SV40-specific serum antibodies were detected in pregnant women at the time of delivery and in cord bloods. There was no evidence of transplacental transmission of SV40. These data indicate that SV40 is circulating at a low prevalence in the northern Italian population long after the use of contaminated vaccines.

Describing the silent human virome with an emphasis on giant viruses

Viruses are the most abundant obligate intracellular entities in our body. Until recently, they were only considered to be pathogens that caused a broad array of pathologies, ranging from mild disease to deaths in the most severe cases. However, recent advances in unbiased mass sequencing techniques as well as increasing epidemiological evidence have indicated that the human body is home to diverse viral species under non-pathological conditions. Despite these studies, the description of the presumably healthy viral flora, i.e. the normal human virome, is still in its infancy regarding viral composition and dynamics. This review summarizes our current knowledge of the human virome under non-pathological conditions.

Human polyomavirus reactivation: disease pathogenesis and treatment approaches

JC and BK polyomaviruses were discovered over 40 years ago and have become increasingly prevalent causes of morbidity and mortality in a variety of distinct, immunocompromised patient cohorts. The recent discoveries of eight new members of the Polyomaviridae family that are capable of infecting humans suggest that there are more to be discovered and raise the possibility that they may play a more significant role in human disease than previously understood. In spite of this, there remains a dearth of specific therapeutic options for human polyomavirus infections and an incomplete understanding of the relationship between the virus and the host immune system. This review summarises the human polyomaviruses with particular emphasis on pathogenesis in those directly implicated in disease aetiology and the therapeutic options available for treatment in the immunocompromised host.