Hepatitis C and HIV detection by blood RNA-sequencing in cohort of smokers

Abstract

Detection of viruses by RNA and DNA sequencing has improved the understanding of the human virome. We sought to identify blood viral signatures through secondary use of RNA-sequencing (RNA-seq) data in a large study cohort. The ability to reveal undiagnosed infections with public health implications among study subjects with available sequencing data could enable epidemiologic surveys and may lead to diagnosis and therapeutic interventions, leveraging existing research data in a clinical context. We detected viral RNA in peripheral blood RNA-seq data from a COPD-enriched population of current and former smokers. Correlation between viral detection and both reported infections and relevant disease outcomes was evaluated. We identified Hepatitis C virus RNA in 228 subjects and HIV RNA in 30 subjects. Overall, we observed 31 viral species, including Epstein-Barr virus and Cytomegalovirus. We observed an enrichment of Hepatitis C and HIV infections among subjects reporting liver disease and HIV infections, respectively. Higher interferon expression scores were observed in the subjects with Hepatitis C and HIV infections. Through secondary use of RNA-seq from a cohort of current and former smokers, we detected peripheral blood viral signatures. We identified HIV and Hepatitis C virus (HCV), highlighting potential public health implications for the approach described this study. We observed correlations with reported infections, chronic infection outcomes and the host transcriptomic response, providing evidence to support the validity of the approach.

Returning incidentally discovered Hepatitis C RNA-seq results to COPDGene study participants

“…Although 30/31 participants (97%) in the HCV Follow-Up Study either reported a previous or received a new HCV diagnosis, the false-positive and false-negative rates for the research HCV RNA-seq results for predicting clinically confirmed HCV are uncertain since the HCV status of participants who did not participate in the HCV Follow-Up Study was not systematically ascertained. We did not perform clinical HCV testing on previously collected COPDGene samples for several reasons: 1) The study consent form did not specify that HCV clinical testing would be performed; 2) We believed that the available evidence from our previously published article on viral sequence detection suggested that the HCV RNA-seq results were likely at least reasonably accurate 14 ; and 3) Since the samples were not handled with a CLIA chain of custody, clinical testing would be required to confirm the results. However, the high percentage of participants who spontaneously volunteered a previous HCV diagnosis at the initial phone call suggests that the research HCV RNA-seq test is likely at least reasonably accurate for clinical HCV.…”

“…As recently reported 14 , 228 COPDGene participants with suggestive evidence of HCV (defined as “HCV results”) were identified by applying PathSeq 26 to blood RNA-seq reads that were not mapped to the human genome. As shown in Table 1 , we developed a procedure for returning HCV results, which separated the clinically important notification about potential HCV infection from a follow-up research study regarding the downstream effects of the return of results.…”

“…COPDGene, an NHLBI-funded observational longitudinal study focused on chronic obstructive pulmonary disease (COPD) 13 , obtained whole blood transcriptomics to investigate COPD pathobiology and heterogeneity. In subsequent analysis of these blood RNA-seq data for non-human transcripts 14 , 228 individuals with suggestive evidence for hepatitis C virus (HCV) were discovered in a research laboratory that was not governed by the Clinical Laboratory Improvements Amendments of 1988 (CLIA). These results were unanticipated, and they provided both an opportunity and a challenge for returning results with personal and public health implications to COPDGene study participants.…”

Blood transcriptomics analysis offers insights into variant-specific immune response to SARS-CoV-2

“…Peripheral blood is the tissue of choice in clinical diagnostics and biomedical research due to minimally invasive sample collection. As blood perfuses all organs, it provides insights into various diseases and medical conditions 1,2 . In general, we can investigate active pathways and organismal responses to stimuli (e.g., a viral infection) on a transcriptomic level 3,4 by using well-established sequencing techniques such as bulk RNA sequencing (RNA-seq).…”