Project description:By unbiased deep sequencing, we identified a novel, highly divergent polyomavirus, provisionally named MX polyomavirus (MXPyV), in stool samples from children. From Mexico, 12 samples (out of 96) were positive for MxPyV by MXPyV-specific PCR. We used the ViroChip microarray and PCR to screen these 12 samples for co-infection with common diarrheal viruses. Six of 12 MxPyV-positive diarrheal samples tested negative by the ViroChip and PCR, and the other 6 samples were positive for at least one known diarrheal virus. The ViroChip microarray (version 5.0, Viro5AG-60K platform, GPL15905) was used to screen RNA extracts from MX polyomavirus (MXPyV)-positive pediatric diarrheal samples from Mexico for common diarrheal viruses.
Project description:WU polyomavirus was detected in nasopharyngeal aspirates in 2 (2.5%) of 79 children with respiratory infections (both infected with respiratory syncytial virus) and in 5 (6.4%) of 78 asymptomatic children during the same winter season in Canada. The strains were closely related to Australian and American viruses based on analysis of large T antigen (TAg) and VP2 genes. The pathogenic role of WU virus is still uncertain.
Project description:We have used deep sequencing to follow polyomavirus infection of mouse NIH3T6 cells. We carried out RNA-seq at various times after infection and analyzed the host transcriptomes. Alignment of sequencing reads to the host genome showed that by late times in infection, 359 host transcripts were seen to be upregulated and 857 were downregulated more than 1.5 fold.
Project description:By unbiased deep sequencing, we identified a novel, highly divergent polyomavirus, provisionally named MX polyomavirus (MXPyV), in stool samples from children. From Mexico, 12 samples (out of 96) were positive for MxPyV by MXPyV-specific PCR. We used the ViroChip microarray and PCR to screen these 12 samples for co-infection with common diarrheal viruses. Six of 12 MxPyV-positive diarrheal samples tested negative by the ViroChip and PCR, and the other 6 samples were positive for at least one known diarrheal virus.
Project description:JC polyomavirus (circular genome) contains two opposite coding regions separated by the regulator non-coding control region (NCCR). NCCR rearrangements and missense mutations in the viral capsid protein VP1 gene differentiate JCV prototype genomes recovered from PML lesions from archetype urine strains. To further investigate the emerging variability of JCV populations in PML, we deep sequenced JCV whole genome recovered from CNS and/or urine samples from HIV- and non HIV-infected PML patients, using single-molecule real-time sequencing (PacBio, Pacific Biosciences). Phylogenetic analysis showed that PML strains distributed among 6 of 7 known genotypes. Whole genome single molecule sequencing provides insight in the genesis of JCV neurotropic populations.
