The prevalence of STL polyomavirus in stool samples from Chinese children

DNA and seroprevalence study of MW and STL polyomaviruses

The clinical importance and the pathogenesis of the MW and STL polyomaviruses (PyVs) remain unclear. Our aim was to study the seroprevalence of MWPyV and STLPyV, and to examine the prevalence of viral DNA in respiratory samples and secondary lymphoid tissues. In total, 618 serum samples (0.8-90 years) were analyzed for seroprevalence. For the DNA prevalence study, 146 patients (2.5-37.5 years) were sampled for adenoids (n = 100), tonsils (n = 100), throat swabs (n = 146), and middle ear discharge (n = 15) in study Group 1. In Group 2, we analyzed 1130 nasopharyngeal samples from patients (0.8-92 years) tested for SARS-CoV-2 infection. The adult seropositivity was 54% for MWPyV, and 81.2% for STLPyV. Both seroprevalence rates increased with age; however, the majority of STLPyV primary infections appeared to occur in children. MWPyV was detected in 2.7%-4.9% of respiratory samples, and in a middle ear discharge. STLPyV DNA prevalence was 1.4%-3.4% in swab samples, and it was detected in an adenoid and in a middle ear discharge. The prevalence of both viruses was significantly higher in the children. Noncoding control regions of both viruses and the complete genomes of STLPyV were sequenced. MWPyV and STLPyV are widespread viruses, and respiratory transmission may be possible.

Lack of detection of HPyV12 DNA using real-time PCR in Italian infants with diarrhea

BACKGROUND

HPyV12 was found in organs of the digestive tract, in particular the liver but also in colon, rectum and feces. Until now, the prevalence of HPyV12 is not well characterized.

METHODS

In this study, we investigate the presence of this novel polyomavirus DNA in stool specimens collected from under-five-year-old children with gastroenteritis compared to healthy infants. A total of 190 fecal specimens previously screened for rotavirus (RV) and adenovirus (ADV) and 80 fecal samples from healthy infants, were tested for HPyV12 DNA using a home-made real time PCR. All fecal specimens were tested for the presence of HPyV12 with specific primers and probes.

RESULTS

None of 190 (0%) episodes of acute gastroenteritis was associated with HPyV12. We did not detect HPyV12 DNA in any of 80 control subjects, as well.

CONCLUSIONS

Our study represents a pilot study aiming to clarify the current epidemiological pattern in pediatric Italian patients regarding the novel and rare HPyV12. Based on our negative data and the recent observations reported in literature, doubts remain on human tropism of the HPyV12 and epidemiology: these issues need further investigations.

Global molecular prevalence and genotype distribution of Sapovirus in children with gastrointestinal complications: A systematic review and meta-analysis

Sapovirus (SaV) is an emerging cause of children gastrointestinal complications such as acute gastroenteritis (AGE). The aim of the present systematic review and meta-analysis was to estimate the global prevalence of the SaV in children and association of infection with SaVs and AGE in children based on case-control studies. Four international databases (PubMed, Scopus, Web of Sciences and Google Scholar) were used to retrieve English-language studies published between January 2000 and December 2020. Comprehensive Meta-Analysis software was applied to estimate the overall prevalence, publication bias and heterogeneity index. The pooled prevalence of SaV infection among children with gastroenteritis was 3.4% [95% confidence interval (CI): 2.9%-3.9%] based on a random-effects meta-analysis. Genogroup I was the dominant genogroup of SaV in children with gastroenteritis [2.2% (95% CI: 1.6%-3.0%)], association analysis showed that SaV was associated with gastroenteritis [OR: 1.843 (95% CI: 1.27-2.66)]. Given the significant prevalence of the virus in children, it is necessary to pay more attention to this situation. Therefore, preventive health measures in children should be a priority.

Genetic Diversity of the Noncoding Control Region of the Novel Human Polyomaviruses

The genomes of polyomaviruses are characterized by their tripartite organization with an early region, a late region and a noncoding control region (NCCR). The early region encodes proteins involved in replication and transcription of the viral genome, while expression of the late region generates the capsid proteins. Transcription regulatory sequences for expression of the early and late genes, as well as the origin of replication are encompassed in the NCCR. Cell tropism of polyomaviruses not only depends on the appropriate receptors on the host cell, but cell-specific expression of the viral genes is also governed by the NCCR. Thus far, 15 polyomaviruses have been isolated from humans, though it remains to be established whether all of them are genuine human polyomaviruses (HPyVs). The sequences of the NCCR of these HPyVs show high genetic variability and have been best studied in the human polyomaviruses BK and JC. Rearranged NCCRs in BKPyV and JCPyV, the first HPyVs to be discovered approximately 30 years ago, have been associated with the pathogenic properties of these viruses in nephropathy and progressive multifocal leukoencephalopathy, respectively. Since 2007, thirteen novel PyVs have been isolated from humans: KIPyV, WUPyV, MCPyV, HPyV6, HPyV7, TSPyV, HPyV9, HPyV10, STLPyV, HPyV12, NJPyV, LIPyV and QPyV. This review describes all NCCR variants of the new HPyVs that have been reported in the literature and discusses the possible consequences of NCCR diversity in terms of promoter strength, putative transcription factor binding sites and possible association with diseases.

Human polyomaviruses 10 and 11 in faecal samples from Brazilian children

The human polyomaviruses (HPyVs) 10 and 11 have been detected in faecal material and are tentatively associated with diarrhoeal disease. However, to date, there are insufficient data to confirm or rule out this association, or even to provide basic information about these viruses, such as how they are distributed in the population, the persistence sites and their pathogenesis. In this study, we analysed stool specimens from Brazilian children with and without acute diarrhoea to investigate the excretion of HPyV10 and HPyV11 as well as their possible associations with diarrhoea. A total of 460 stool specimens were obtained from children with acute diarrhoea of unknown aetiology, and 106 stool specimens were obtained from healthy asymptomatic children under 10 years old. Samples were collected during the periods of 1999-2006, 2010-2012 and 2016-2017, and found previously to be negative for other enteric viruses and bacteria. The specimens were screened for HPyV10 and HPyV11 DNA by the polymerase chain reaction (PCR). Randomly selected positive samples were sequenced to confirm the presence of HPyV10 and HPyV11. The sequenced strains showed a percent of nucleotide identity of 93.4-99.6% and 85.5-98.9% with the reference HPyV10 and HPyV11 strains, respectively, confirming the PCR results. HPyV10 and HPyV11 were detected in 7.2% and 4.7% of the stool specimens from children with and without diarrhoea, respectively. The prevalence of both viruses was the same among children with diarrhoea and healthy children. There was also no difference between boys and girls or the degree of disease (severe, moderate or mild) among groups. Phylogenetic analysis showed that all of the genotypes described so far for HPyV10 and HPyV11 circulate in Rio de Janeiro. Our results do not support an association between HPyV10 and HPyV11 in stool samples and paediatric gastroenteritis. Nevertheless, the excretion of HPyV10 and HPyV11 in faeces indicates that faecal-oral transmission is possible.

An overview on human polyomaviruses biology and related diseases

In recent years, the Polyomaviridae family grew rapidly, thanks to the introduction of high-throughput molecular techniques. To date, 14 polyomaviruses have been identified in humans but the association with human diseases has been established only for few of them. BKPyV has been associated with nephropathy in kidney transplant patients and hemorrhagic cystitis in hematopoietic stem cell transplant patients; JCPyV to progressive multifocal leukoencephalopathy, mainly in HIV-positive patients; Merkel cell polyomavirus to Merkel cell carcinoma; Trichodysplasia spinulosa polyomavirus to the rare skin disease Trichodysplasia spinulosa; human polyomaviruses 6 and 7 to pruritic rash. Immunocompromised patients are at risk of developing disease. Here, we summarized and discussed the scientific literature concerning the human polyomaviruses biology, seroprevalence and association with human diseases.

Merkel cell polyomavirus and Merkel cell carcinoma

Merkel cell polyomavirus (MCPyV) causes the highly aggressive and relatively rare skin cancer known as Merkel cell carcinoma (MCC). MCPyV also causes a lifelong yet relatively innocuous infection and is one of 14 distinct human polyomaviruses species. Although polyomaviruses typically do not cause illness in healthy individuals, several can cause catastrophic diseases in immunocompromised hosts. MCPyV is the only polyomavirus clearly associated with human cancer. How MCPyV causes MCC and what oncogenic events must transpire to enable this virus to cause MCC is the focus of this essay.This article is part of the themed issue 'Human oncogenic viruses'.

Establishment and Application of a Universal Coronavirus Screening Method Using MALDI-TOF Mass Spectrometry

There are four human coronaviruses (HCoVs), distributed worldwide, that are associated with a range of respiratory symptoms. The discovery of severe acute respiratory syndrome (SARS)-CoV and Middle East respiratory syndrome (MERS)-CoV shows that HCoVs pose a significant threat to human health. Our work aims to develop a sensitive method (mCoV-MS) which can not only identify known HCoVs accurately, but also have the ability to provide clues for the emerging HCoVs. The method was performed using a MassARRAY matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) system. We developed a 17-plex analysis to detect six HCoVs in Panel A and another 17-plex analysis to detect Alphacoronavirus and Betacoronavirus in Panel B. All tested primers and probes for the mCoV-MS method were effective, with no cross-reactivity observed with other common respiratory viruses. To confirm the usefulness of the mCoV-MS method we screened 384 pharyngeal and/or anal swab samples collected from bats/rodents, and 131 nasal and throat swabs from human patients. The results showed good concordance with the results of metagenomic analysis or PCR-sequencing. The validation test showed mCoV-MS method can detect potentially pathogenic CoVs in Alphacoronavirus and Betacoronavirus and provide convincingly phylogenetic evidences about unknown CoVs. The mCoV-MS method is a sensitive assay that is relatively simple to carry out. We propose that this method be used to complement next generation sequencing technology for large-scale screening studies.

Isolation and characterization of a novel putative human polyomavirus

The small double-stranded DNA polyomaviruses (PyVs) form a family of 73 species, whose natural hosts are primarily mammals and birds. So far, 13 PyVs have been isolated in humans, and some of them have clearly been associated with several diseases, including cancer. In this study, we describe the isolation of a novel PyV in human skin using a sensitive degenerate PCR protocol combined with next-generation sequencing. The new virus, named Lyon IARC PyV (LIPyV), has a circular genome of 5269 nucleotides. Phylogenetic analyses showed that LIPyV is related to the raccoon PyV identified in neuroglial tumours in free-ranging raccoons. Analysis of human specimens from cancer-free individuals showed that 9 skin swabs (9/445; 2.0%), 3 oral gargles (3/140; 2.1%), and one eyebrow hair sample (1/439; 0.2%) tested positive for LIPyV. Future biological and epidemiological studies are needed to confirm the human tropism and provide insights into its biological properties.

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.

Viruses Causing Gastroenteritis: The Known, The New and Those Beyond

The list of recently discovered gastrointestinal viruses is expanding rapidly. Whether these agents are actually involved in a disease such as diarrhea is the essential question, yet difficult to answer. In this review a summary of all viruses found in diarrhea is presented, together with the current knowledge about their connection to disease.

MW polyomavirus and STL polyomavirus present in tonsillar tissues from children with chronic tonsillar disease

We aimed to explore the frequency of all 13 human polyomaviruses (HPyVs), especially MW polyomavirus (MWPyV) and STL polyomavirus (STLPyV), in tonsillar tissues from Chinese children with chronic tonsillar disease. We examined 99 swabs from mucosal surfaces of palatine tonsils, in which six HPyVs were detected. MWPyV and STLPyV were each detected in two samples. This provides new evidence for the hypothesis that the lymphoid system may play a role in HPyV infection and persistence. We need to define their role in tonsillar disease in the future.

Application of Multiplex PCR Coupled with Matrix-Assisted Laser Desorption Ionization-Time of Flight Analysis for Simultaneous Detection of 21 Common Respiratory Viruses

Respiratory infections continue to pose a significant threat to human health. It is important to accurately and rapidly detect respiratory viruses. To compensate for the limits of current respiratory virus detection methods, we developed a 24-plex analysis (common respiratory virus-mass spectrometry [CRV-MS]) that can simultaneously detect and identify 21 common respiratory viruses based on a matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry system. To evaluate the efficacy of the CRV-MS method, we used 102 samples that were confirmed positive for these common respiratory viruses. All tests using the CRV-MS method were effective, with no cross-reactivity observed with other common respiratory viruses. To confirm the usefulness of the CRV-MS method, we screened 336 nasal and throat swabs that were collected from adults or children with suspected viral acute respiratory tract infections using the CRV-MS method and consensus PCR/reverse transcription-PCR (RT-PCR) methods. Excluding four RNase P-negative samples, the CRV-MS and consensus PCR/RT-PCR methods detected respiratory viruses in 92.5% (307/332) and 89.5% (297/332) of the samples, respectively. The two methods yielded identical results for 306 (92.2%) samples, including negative results for 25 samples (7.5%) and positive results for 281 samples (84.6%). Differences between the two methods may reflect their different sensitivities. The CRV-MS method proved to be sensitive and robust, and it can be used in large-scale epidemiological studies of common respiratory virus infections.