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Viral risk factors in ME/CFS

Study Aim

This project aims to characterize viral factors associated with immune responses and inflammation in ME/CFS.

Investigators

  • Dawei Li, PhD
  • Ronald Davis, PhD

Updates and Potential

  • In our blood virome screen analysis, we used multiple methods including our original viral integration method and analyzed pilot ME/CFS sequencing data. We identified partial genome sequences from common viruses in ME/CFS. We are now constructing a larger virome database to update the screen and plan to publish.
  • We developed a novel machine learning tool, VirusPredictor, to predict among infectious virus, ERV, and non-ERV human sequences. This tool has the potential to find unknown viruses. It was published in Bioinformatics in 2024 and the software is freely available. We are using this tool to analyze ME/CFS data.
  • In our ERV variant study, we developed a new analytic approach and genotyped genome-wide ERVs in pilot ME/CFS samples. We found associations with ME/CFS-related measures. We are working on a manuscript.
  • We recently developed a novel method to model ERV variants. This can be used to generate ground truth ERVs for benchmarking ERV detection and genotyping. The software is freely available. The manuscript is under review in PLOS Computational Biology, pending editor final decision.
STUDY HYPOTHESIS AND DESCRIPTION

Viral triggers of immune response in ME/CFS have long been speculated but remain poorly understood. Germline endogenous retroviruses (ERVs) and somatic viral infections both have significant impacts on immune response and have been studied for years; however, the previous studies mainly focused on commonly tested viral pathogens or several known ERV candidates. Not surprisingly, none has been proven to be common to ME/CFS patients. A comprehensive analysis of the full spectrum of ERVs and the virome is likely to change our understanding of the roles of ERVs and viral infections in ME/CFS. This proposal is aimed to develop novel algorithms to investigate the contributions of genome-wide ERVs and the human virome to ME/CFS.

OBJECTIVES

Two young intercultural professionals in whitecoats discussing microchip scheme while one of them pointing at computer screen

  1. Investigate somatic viral infections (such as the human virome and virome-wide viral infections) and germline viral sequences (such as endogenous retrovirus variants) in patient genomes.
  2. Develop the analytic methods based on a novel algorithm and apply it to the pilot dataset from ME/CFS patients.
  3. Identify viral factors associated with ME/CFS and/or related phenotypes.

Consent management

Consent Preferences

Data Subject Access Request (DSAR) Form 

Myalgic Encephalomyelitis / Chronic Fatigue Syndrome (ME / CFS) Post Treatment Lyme Disease Syndrome (PTLDS), Fibromyalgia Leading Research. Delivering Hope.Open Medicine Foundation®

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