Project description:Human herpesvirus 6 (HHV-6) A and B are highly ubiquitous betaherpesviruses, infecting the majority of the human population. Like other herpesviruses, our understanding of their protein coding potential is far from complete. Here we use ribosome profiling and RNA-seq to experimentally define the HHV-6 translation products and to follow their temporal expression. We identified hundreds of new open reading frames (ORF)s, including many upstream ORFs (uORF)s and internal ORFs (iORF)s, generating a complete atlas of HHV-6 translation products. Integrating data from human cytomegalovirus we uncover numerous uORFs and iORFs that are conserved between beta herpesviruses and we show uORFs are specifically enriched in late viral genes. We also identified three highly abundant viral long non coding RNAs (lncRNA)s and we show one of these lncRNAs generate a non-polyadenylated stable intron that is conserved between all sequenced beta herpesviruses. Overall, this work uncovers the full complexity of the HHV-6 family genomes and highlights novel features that are conserved between beta herpesviruses, providing a resource for future functional studies.
Project description:Limited understanding of the immunopathogenesis of human herpesvirus 6B (HHV-6B) has prevented its acceptance as a pulmonary pathogen after hematopoietic cell transplantation (HCT). We conducted a prospective multicenter study of patients undergoing bronchoalveolar lavage (BAL) for pneumonia after allogeneic HCT. We tested blood and BAL fluid (BALF) for HHV-6B DNA and mRNA transcripts associated with lytic infection and performed RNA-seq on paired blood. Among 116 participants, HHV-6B DNA was detected in 37% of BALs, 49% of which had HHV-6B mRNA detection. We established an HHV-6B DNA threshold (≥2.3 log10copies/ml in BALF) that was highly predictive of HHV-6B mRNA detection and increased risk for death from respiratory failure (adjusted HR, 2.35; 95% CI, 1.08-5.11). Participants with HHV-6B DNA in BALF exhibited distinct host gene expression signatures, notable for enriched interferon signaling pathways in participants clinically diagnosed with idiopathic pneumonia. These data implicate HHV-6B as a pulmonary pathogen after allogeneic HCT.
Project description:We report the application of size selection of small RNA species isolated from Jjhan cells harboring the human herpesvirus 6A genome. We ammassed >3.4million reads of sequence from three different sources: Normal Brain cell total RNA, Jjhan total RNA and HHV-6A BAC transfected Jjhan total RNA. Sequences were mapped to the HHV-6A Uganda 1102 strain genome (GenBank: X83413.1) with no less than 100% match for reads >20nt and <23nt. The resulting pool of candidates was mapped to the HHV-6A genome. Single pass 36nt sequencing of samples either with or without HHV-6a genomes present.
Project description:To determine if HHV-6A infection affects cell metabolism of host cells, we conducted a global RNA sequencing analysis in HHV-6A infected cells
Project description:In order to understand the effect of HHV-6A reactivation on host cell, U2-OS bone osteosarcoma cells were generated carrying latent HHV-6A genome. These cells were either treated with DMSO (solvent control) or Trichostatin-A (TSA) for viral reactivation. As a control cells carrying no HHV-6A were used and treated similarly. Two biological replicates of each sample were processed for small RNA transcriptomics (small RNAseq). Furthermore, HeLa (cervical epithelial cells) were generated carrying lentiviral insertions of one of the small non-coding RNA from HHV-6A (sncRNA-U14). These cells could be transiently induced for sncRNA-U14 transcription using Doxycycline. HeLa cells having a mock lentiviral backbone was used as a control and was treated similarly. Two biological replicates of each sample were processed for small RNA transcriptomics (small RNAseq).
Project description:We report the application of size selection of small RNA species isolated from Jjhan cells harboring the human herpesvirus 6A genome. We ammassed >3.4million reads of sequence from three different sources: Normal Brain cell total RNA, Jjhan total RNA and HHV-6A BAC transfected Jjhan total RNA. Sequences were mapped to the HHV-6A Uganda 1102 strain genome (GenBank: X83413.1) with no less than 100% match for reads >20nt and <23nt. The resulting pool of candidates was mapped to the HHV-6A genome.