Viral dysbiosis in children with new-onset celiac disease

Viruses are common components of the intestinal microbiome, modulating host bacterial metabolism and interacting with the immune system, with a possible role in the pathogenesis of immune-mediated diseases such as celiac disease (CeD). The objective of this study was to characterize the virome profile in children with new-onset CeD. We used metagenomic analysis of viral DNA in mucosal and fecal samples from children with CeD and controls and performed sequencing using the Nextera XT library preparation kit. Abundance log2 fold changes were calculated using differential expression and linear discriminant effect size. Shannon alpha and Bray–Curtis beta diversity were determined. A total of 40 children with CeD and 39 controls were included. We found viral dysbiosis in both fecal and mucosal samples. Examples of significantly more abundant species in fecal samples of children with CeD included Human polyomavirus 2, Enterobacteria phage mEpX1, and Enterobacteria phage mEpX2; whereas less abundant species included Lactococcus phages ul36 and Streptococcus phage Abc2. In mucosal samples however, no species were significantly associated with CeD. Shannon alpha diversity was not significantly different between CeD and non-CeD groups and Bray–Curtis beta diversity showed no significant separation between CeD and non-CeD samples in either mucosal or stool samples, whereas separation was clear in all samples. We identified significant viral dysbiosis in children with CeD, suggesting a potential role in the pathogenesis of CeD indicating the need for further studies.

Complete Response to Nivolumab in Recurrent/Metastatic HPV-Positive Head and Neck Squamous Cell Carcinoma Patient After Progressive Multifocal Leukoencephalopathy: A Case Report

In an immune-competent context nivolumab showed long-term benefit in overall survival in recurrent/metastatic head and neck squamous cell carcinoma (HNSCC); however, in special cancer population such as these patients with immunodeficiency and viral infections, data on checkpoint inhibitors (ICI) activity are scant. Herein, we report a patient with a Human papilloma virus (HPV)-related oropharyngeal cancer (OPC) and CD4 lymphocytopenia. After a first-line treatment complete remission, the patient experienced Human Polyomavirus (JCV) infection in the brain. Consequently, to the recovery from progressive multifocal leukoencephalopathy (PML) the patient metastasized and was enrolled in a single-arm trial with nivolumab (EudraCT number: 2017-000562-30). A complete and durable response (more 3 years) was observed after 10 nivolumab injections Q2wks, interrupted for persistent drug related G2 diarrhea and a syndrome of inappropriate antidiuretic hormone secretion. We describe the circulating immune profile (before-, during-, and after nivolumab), consistent with the clinical history. Moreover, during nivolumab treatment, brain MRI evidenced the presence of small punctuate areas of contrast enhancement, reflecting a mild immune response in perivascular spaces. By cytofluorimetry, we observed that during JCV infection the CD4/CD8 ratio of the patient was under the normal values. After JCV infection recovery and before nivolumab treatment, CD4/CD8 ratio reached the normality threshold, even if the CD4+ T cell count remained largely under the normal values. During ICI, gene expression xCell analyses of circulating immune cells of the patient, showed a progressive normalization of the total immune profile, with significant boost in CD4+ and CD8+ T cells and a reduction in NK T, comparable to the circulating immune profile of reference tumor-free HNSCC patients. The present case supports the activity of ICI in a population of special cancer patients; whether JCV and HPV infections (alone or together) might have a possible role as immune booster(s), require further investigations.

Innovative therapeutic concepts of progressive multifocal leukoencephalopathy

Progressive multifocal leukoencephalopathy (PML) is an opportunistic viral disease of the brain—caused by human polyomavirus 2. It affects patients whose immune system is compromised by a corresponding underlying disease or by drugs. Patients with an underlying lymphoproliferative disease have the worst prognosis with a mortality rate of up to 90%. Several therapeutic strategies have been proposed but failed to show any benefit so far. Therefore, the primary therapeutic strategy aims to reconstitute the impaired immune system to generate an effective endogenous antiviral response. Recently, anti-PD-1 antibodies and application of allogeneic virus-specific T cells demonstrated promising effects on the outcome in individual PML patients. This article aims to provide a detailed overview of the literature with a focus on these two treatment approaches.

The differential presence of human polyomaviruses, JCPyV and BKPyV, in prostate cancer and benign prostate hypertrophy tissues

Background Studies have shown that human polyomavirus infection may be associated with various human cancers. We investigated the potential relationship between the prevalence of JCPyVor BKPyV and prostate cancer (PC) in patients from Taiwan. Methods Patients with PC and benign prostate hypertrophy (BPH; 76 and 30 patients, respectively) were recruited for this study. Paraffin-embedded tissues and clinical information of the patients were obtained. The tissue sections were used for viral DNA detection and immunohistochemistry analysis was performed for examining viral large T (LT) and VP1 proteins. Regression analysis was used to evaluate the relationship between the clinical characteristics of the patients and the risk of JCPyV/BKPyV infection. Results The prevalence of JCPyV/BKPyV DNA was different in PC and BPH tissues (27/76 [35.52%] and 2/30 [6.7%], respectively, p = 0.003)]. The LT and VP1 proteins were detected in 27 (35.52%) and 29 PC (38.2%) specimens, respectively, but neither protein was detected in BPH samples (p < 0.001). PC cells were more susceptible to JCPyV infection than BPH tissues [odds ratio (OR) 7.71, 95% CI: 1.71–34.09, p = 0.003). Patients with PC showing high levels of prostate-specific antigen and high Gleason scores were associated with a high risk of viral infection (ORs 1.1, 95% CI 1.000–1.003; p = 0.045 and ORs 6.18, 95% CI 1.26–30.33, p = 0.025, respectively). The expression of LT protein associated with the risk of PC increased 2923.39-fold (95% CI 51.19–166,963.62, p < 0.001). Conclusions The findings indicate that JCPyV infection in PC cells may be associated with prostate cancer progression and prognosis. Graphical abstract

Natural History of Cutaneous Human Polyomavirus Infection in Healthy Individuals

Several human polyomaviruses (HPyVs) were recently discovered. Merkel cell polyomavirus (MCPyV) induces Merkel cell carcinoma. HPyV6, HPyV7, and TSPyV have been associated with rare skin lesions in immunosuppressed patients. HPyV9, HPyV10, and Saint Louis Polyomavirus (STLPyV) have not been convincingly associated with any disease. The aim of this prospective study was to evaluate the cutaneous prevalence, persistence and viral load of HPyVs in healthy individuals. Eight hundred seventy forehead and hand swabs were collected from 109 volunteers 4–6 weeks apart (collection period-1). Fifty-nine participants were available for follow-up a decade later (collection period-2). HPyV-DNA prevalence and viral loads of MCPyV, HPyV6, HPyV7, TSPyV, HPyV9, HPyV10, and STLPyV were determined by virus-specific real-time PCRs. Risk factors for HPyV prevalence, short- and long-term persistence were explored by logistic regression analyses. Baseline prevalence rates were similar for forehead and hand: MCPyV 67.9/67.0%, HPyV6 31.2/25.7%, HPyV7 13.8/11.0%, HPyV10 11.9/15.6%, STLPyV 7.3/8.3%, TSPyV 0.9/0.9%, and HPyV9 0.9/0.9%. Short-term persistence in period-1 was found in 59.6% (MCPyV), 23.9% (HPyV6), 10.1% (HPyV7), 6.4% (HPyV10), 5.5% (STLPyV), and 0% (TSPyV and HPyV9) on the forehead, with similar values for the hand. Long-term persistence for 9–12 years occurred only for MCPyV (forehead/hand 39.0%/44.1% of volunteers), HPyV6 (16.9%/11.9%), and HPyV7 (3.4%/5.1%). Individuals with short-term persistence had significantly higher viral loads at baseline compared to those with transient DNA-positivity (p &lt; 0.001 for MCPyV, HPyV6, HPyV7, and HPyV10, respectively). This was also true for median viral loads in period-1 of MCPyV, HPyV6, and HPyV7 of volunteers with long-term persistence. Multiplicity (two or more different HPyVs) was a risk factor for prevalence and persistence for most HPyVs. Further risk factors were older age for HPyV6 and male sex for MCPyV on the forehead. Smoking was not a risk factor. In contrast to MCPyV, HPyV6, HPyV7, and rarely STLPyV, polyomaviruses TSPyV, HPyV9, and HPyV10 do not seem to be long-term constituents of the human skin virome of healthy individuals. Furthermore, this study showed that higher viral loads are associated with both short- and long-term persistence of HPyVs on the skin. HPyV multiplicity is a risk factor for prevalence, short-term and/or long-term persistence of MCPyV, HPyV6, HPyV7, and HPyV10.

Renal Failure Associated with Human Polyomavirus BK and Human Adenovirus in a Child with Acute Lymphoblastic Leukaemia

Immunocompromised patients are susceptible to multiple severe viral infections. This paper describes a 4-year-old boy with newly diagnosed B-cell precursor acute lymphoblastic leukaemia. The 4-year-old patient developed haemorrhagic cystitis, obstructive nephropathy and renal failure due to human polyomavirus BK and human adenovirus co-infection. Cidofovir should be used only in life-threatening cases.

Prevalence of Human Polyomavirus BK Virus in Prostate Cancer Patients and Benign Prostatic Hyperplasia: A Cross-Sectional Study on Prostate Patients Referred to Imam Khomeini Hospital in Ahvaz Between 2015 and 2017

Background: Human polyomavirus BK virus (BKV) belongs to the Polyomaviridae family and seems to be a drastic virus in prostate cancer (PCa) etiology. BKV induces oncogenesis via the expression of large tumor antigen (LTAg) and small tumor antigen (stAg). Also, BKV infection seems to play an essential role in prostate cancer development. Objectives: In this study was aimed to study the prevalence of BKV in benign and cancerous prostate tissues. Methods: In this study, 100 formalin-fixed paraffin-embedded tissues of PCa specimens and benign prostatic hyperplasia (BPH) were collected. The DNA was extracted from tissue samples, and the BKV DNA was investigated using a semi-nested polymerase chain reaction (PCR). The MEGA 6.0 software was used for phylogenetic analysis to assemble the viral genome. A phylogenetic tree was constructed by neighbor-joining analysis with 1,000 replicates of the bootstrap resampling test using Mega 6.0. Statistical analysis was done by SPSS version 22. Results: The BKV DNA was found in 66% (33/50) of patients with PCa and 36% (18/50) of patients with benign prostatic hyperplasia (BPH) (P = 0.003). The frequency of BKV DNA in different classes of Gleason score (5 - 10) was not significant (0.094). The distribution of BKV DNA among different age groups was not significant (P = 0.086). Conclusions: High frequency of BKV infection was detected in patients with PCa compared to patients with BPH (P = 0.003), and the coexistence of BKV DNA was confirmed in 51% (51/100) of tissue samples, which were confirmed to be subtype 1 of BKV infection.

Tracking SARS-CoV-2 in rivers as a tool for epidemiological surveillance

The aim of this work was to evaluate if rivers could be used for SARS-CoV-2 surveillance to support health authorities. Five sampling points from three rivers (AR-1 and AR-2 in Arenales River, MR-1 and MR-2 in Mojotoro River, and CR in La Caldera River) from the Province of Salta (Argentina), two of them receiving the discharges of the wastewater plants (WWTP) of the city of Salta, were monitored from July to December 2020 during the first wave of COVID-19. Fifteen water samples from each point (75 samples in total) were collected and characterized physico-chemically and microbiologically and SARS-CoV-2 was quantitatively detected by RT-qPCR. In addition, two targets linked to human contributions, human polyomavirus (HPyV) and RNase P, were quantified and used to normalize the SARS-CoV-2 concentration, which was ultimately compared to the active reported COVID-19 cases. Statistical analyses allowed us to verify the correlation between SARS-CoV-2 and the concentration of fecal indicator bacteria (FIB), as well as to find similarities and differences between sampling points. La Caldera River showed the best water quality, and FIB were within acceptable limits for recreational activities. Although Mojotoro River receives the discharge of the northern WWTP of the city, it did not affect the water quality. Instead, the Arenales River presented the poorest water quality and the river at AR-2 was negatively affected by the discharges of the southern WWTP, which contributed to the significant increase of fecal contamination. SARS-CoV-2 was only found in about half of the samples and in low concentrations in La Caldera and Mojotoro Rivers, while it was high and persistent in the Arenales River. None of the two human tracers was detected in CR, only HPyV was found in MR-1, MR-2 and AR-1, and both were quantified in AR-2. The experimental and the normalized (using the two tracers) viral concentrations strongly correlated with the curve of active reported COVID-19 cases; thus, the Arenales River at AR-2 reflected the epidemiological situation of the city. This is, to the best of our knowledge, the first study that showed the dynamic of SARS-CoV-2 concentration in an urban river highly impacted by wastewater and proved that can be used for SARS-CoV-2 surveillance to support health authorities.