The project/pipeline brings together an expert virology, microbiology, and pathology team to characterize viral/bacterial pathogens, immune cell activity, and human gene expression in tissue samples collected from patients with LongCovid and ME/CFS. Potential pathogens in the tissues will be identified with computational-based approaches such as whole genome/transcriptome sequencing and spatial transcriptomics. Tissue types analyzed by the pipeline include intestinal tissue and lung tissue collected from LongCovid patients and skeletal muscle tissue collected from LongCovid and ME/CFS patients. The teams are also performing a similar analysis on small fiber neuropathy tissue samples collected from patients with LongCovid, ME/CFS, Post Treatment Lyme Disease & EDS.

Whenever possible, viruses and other pathogens identified in tissue samples will be studied in concert with activity of the human microbiome in nearby fluids or body sites. For example, the LongCovid lung tissue study will correlate identification of SARS-CoV-2 in lung tissue samples with activity of the lung microbiome in nearby bronchial fluid. Tools used to characterize microbiome activity in both tissue samples and neighboring fluids include metagenomics and metatranscriptomics. These tools will allow the researchers to characterize the activity of identified organisms (the genes they are turning on/off).