Molecular epidemiology of JC polyomavirus in HIV-infected patients and healthy individuals from Iran

Prediction of the Co-receptor usage of the main worldwide HIV-1 subtypes, CRF, and CRF35-AD in Iranian patients via the five genotypic tools

HIV-1 has various subtypes and CRFs, each with unique genetic attributes that impact the virus's spread, disease development, and response to treatment in different populations. Determining V3 tropism is crucial for utilizing CCR5 antagonists and understanding why certain HIV-1 subtypes are more pathogenic than others are. Genotypic coreceptor usage of 603 major subtypes of A, B, C, AE, and CRF35-AD is investigated via five bioinformatics tools (PhenoSeq, WebPSSM, Geno2Pheno, Net charge, and the 11/25 rule). This study examined crown motifs, N-glycosylation sites, and T8V mutations in all subtypes. R5 viruses are common in subtypes A, B, C, and CRF35-AD. These data indicate that R5 viruses in subtypes A and B are more prone to crown motif formation. The first report assessed the tropism of common HIV-1 subtypes and reported that CCR5 inhibitors could help treat patients with all subtypes but not AE. WebPSSM is a suitable method for determining HIV-1 tropism in different subtypes. Finally, large cohorts to assess virological response to CCR5 inhibitors would provide deep insight into the practicality of genotypic methods in clinical settings.

In silico analysis of human herpes virus-8 genome: a comparison of the K1, VR1, and VR2 regions for genotyping and global geographical distribution

Investigations of the K1 gene revealed six main genotypes clustered according to geography. Here, the global distribution and HHV8 genotyping using the K1 gene and two hypervariable regions (VR1 and VR2) were evaluated. We searched GenBank for 6,889 HHV8-K1 genes via various keywords, selecting sequences longer than 730 bp. Afterwards, the VR1 and VR2 regions were derived from the K1 genes, and genotyping of the K1, VR1, and VR2 sequences was performed by applying phylogenetic tree and BioAfrica methods. The K1 genotyping result was most similar to that of VR1, followed by VR2. The most common genotypes and subtypes in the three regions studied were A (A2) and C (C3), which are found in Africa, America, and Asia. Although the A and C genotypes are more predominant, the other genotypes, B, D, E, and F, are more ancient and are commonly found in America, Asia, and Oceania. K1 is commonly used for HHV8 genotyping, but VR1 can be a reliable alternative when long-term PCR amplification is not possible. The genotyping and subtyping results of both methods were very similar (92%), and it can be inferred that both procedures can be applied for HHV-8 genotyping.

Prevalence of JC polyomavirus among rheumatoid arthritis and systemic lupus erythematosus patients and its correlation with vitamin D levels

Background and Objectives

Vitamin D deficiency in viral infection associated with autoimmune diseases is well documented. This study assessed the prevalence of JC virus in patients with rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE), and its correlation with vitamin D level.

Materials and Methods

Serum and urine samples were collected from 50 patients with RA and SLE. DNA was extracted and subjected to PCR test. Positive PCR products were sequenced, phylogenetic tree was constructed to determine the JC virus genotype. The patient's vitamin D level was evaluated.

Results

Of 50 patients, 19 (38%) were diagnosed as RA, and 31 (62%) were identified as SLE. JC virus DNA was detected in 17 (34%) patients' urine samples including 5 (26.3%) RA and 12 (38.7%) SLE cases. JC virus DNA was detected 2 (4%) in patients' serum samples (one RA. and one SLE). JC virus genotype 3A was dominant. Interestingly, the SLE patients with positive JC virus showed lowered vitamin D compared to patients with negative JC virus (P<0.005).

Conclusion

Given the high rate of JC virus, DNA detection and susceptibility of patients for PML development, it is recommended that detection of JC virus DNA and vitamin D level should be implemented for patients with RA/SLE prior to treatment.

John Cunningham Virus and Progressive Multifocal Leukoencephalopathy: A Falsely Played Diagnosis

Progressive Multifocal Leukoencephalopathy (PML) is a possibly fatal demyelinating disease and John Cunningham Polyomavirus (JCPyV) is believed to cause this condition. The so-called JCPyV was initially reported in lymphoma and Human Immunodeficiency Virus (HIV) cases, whereas nowadays, its incidence is increasing in Multiple Sclerosis (MS) cases treated with natalizumab (Tysabri). However, there are conflicting literature data on its pathology and diagnosis, whereas some misdiagnosed reports exist, giving rise to further questions towards the topic. In reality, the so-called PML and the supposed JCPyV are not what they seem to be. In addition, novel and more frequent PML-like conditions may be reported, especially after the Coronavirus Disease 2019 (COVID-19) pandemic.

BK and JC polyomaviruses and risk of urothelial bladder carcinoma: a preliminary study in the northern shores of Persian Gulf, Iran

BACKGROUND

Bladder cancer is a challenging public health concern in South of Iran because of its high prevalence and the related medical expenses. Although the exact etiology of bladder cancer remains unknown, given the cell transforming ability and oncogenic potential of the members of Polyomaviridae families, this study was conducted to evaluate the magnitude of BK polyomavirus (BKPyV) and John Cunningham polyomavirus (JCPyV) among patients with bladder cancer residents in the northern shores of the Persian Gulf, South of Iran.

METHODS

Totally 211 patients with bladder cancer were enrolled in this study. Bladder biopsy samples of these patients and patients with interstitial cystitis as well as autoptic samples of healthy bladder were tested for detection of BKPyV and JCPyV by semi-nested PCR-RFLP followed by sequencing.

RESULTS

BKPyV and JCPyV were detected in 1.7% and 6.1% of bladder cancer samples, respectively. These samples were infected with JCPyV genotypes 2, 3 and 6 and BKPyV genotypes I and IV. BKPyV and JCPyV coinfection was detected in 2 samples. Moreover, one of the healthy bladder samples was positive for BKPyV, and one of the interstitial cystitis samples was positive for JCPyV. Although the majority of infected patients were in the age group 70-79 years, male, residents in Tangestan, stage Ta-T1, and low-grade and high-grade papillary urothelial carcinoma, the prevalence of BKPyV and JCPyV among patients with bladder cancer was not statistically associated with age, gender, place of residency, and stage and grade of the tumor.

CONCLUSION

Despite identifying BKPyV and JCPyV in a number of bladder cancer biopsy specimens and the high prevalence of bladder cancer among people resident in South of Iran, it is suggested that these viruses are unlikely to be effective causative factors in bladder carcinogenesis in this region. Therefore, environmental risk factors and genetic backgrounds may have a more prominent role than human polyomaviruses in the development of bladder cancer in South of Iran.

Discriminating between JCPyV and BKPyV in Urinary Virome Data Sets

Polyomaviruses are abundant in the human body. The polyomaviruses JC virus (JCPyV) and BK virus (BKPyV) are common viruses in the human urinary tract. Prior studies have estimated that JCPyV infects between 20 and 80% of adults and that BKPyV infects between 65 and 90% of individuals by age 10. However, these two viruses encode for the same six genes and share 75% nucleotide sequence identity across their genomes. While prior urinary virome studies have repeatedly reported the presence of JCPyV, we were interested in seeing how JCPyV prevalence compares to BKPyV. We retrieved all publicly available shotgun metagenomic sequencing reads from urinary microbiome and virome studies (n = 165). While one third of the data sets produced hits to JCPyV, upon further investigation were we able to determine that the majority of these were in fact BKPyV. This distinction was made by specifically mining for JCPyV and BKPyV and considering uniform coverage across the genome. This approach provides confidence in taxon calls, even between closely related viruses with significant sequence similarity.