Proteinopathies are neurodegenerative disorders characterized by accumulation of specific misfolded or aggregated proteins in the nervous tissue. Some of the major proteinopathies include prions, Parkinson’s, Alzheimer’s, Huntington’s and dementia. Prion diseases are classical transmissible spongiform encephalopathies (TSEs) characterized by an always fatal, progressive neuronal degeneration in the brain due to infectious misfolded prion proteins. Chronic wasting disease (CWD) is a TSE affecting both wild and captive cervids, such as mule deer, white-tailed deer, elk and moose, with a prolonged incubation period. Hence, we attempted to use an ultrasensitive real-time quaking-induced conversion (RT-QuIC) assay to diagnose CWD using recto-anal mucosa-associated lymphoid tissue (RAMALT) from farmed white-tailed deer. We also employed the RT-QuIC assay with a neuronal cell culture model harboring RML scrapie prion and organotypic slice cultures to investigate how the divalent cation manganese (Mn), whose neurotoxicity has been linked to metal-binding proteins, promotes the aggregation of prion protein and the seeding activity of scrapie prion. Mn altered the aggregation propensity of prions in a linear relationship with the cell density when seeded with prion-infected cells but not for the uninfected cells. Our study unraveled a causal link for protein aggregation in prion proteinopathies by providing evidence of Mn binding to metal-binding domains of the prion protein. Mn can cause neurological, Parkinsonian-like symptoms in occupationally exposed individuals like welders who are chronically exposed to Mn-rich welding fumes. No blood-based biomarkers are available for Mn poisoning in humans except for expensive imaging techniques, like brain MRI. Hence, we used the RT-QuIC assay to detect α-synuclein (αSyn) aggregates present in exosomes isolated from a blinded cohort of serum and plasma samples from a welding fume-exposed population and age-matched controls. Using the RT-QuIC assay, we differentiated welders from controls with >95% sensitivity and specificity, suggesting that exosomal αSyn aggregates may serve as a circulating biomarker for Mn neurotoxicity. Furthermore, next-generation sequencing of serum exosomes showed changes in several small RNAs, such as miRNAs, piRNAs, and tRNAs that may potentially contribute to Mn neurotoxicity and thus could also be developed as potential biomarkers. Next, we further explored performance of the RT-QuIC assay on cerebrospinal fluid, brain homogenate, and submandibular gland homogenate samples from clinically confirmed PD and control subjects. We differentiated the synucleinopathy cases from control subjects with sensitivities and specificities exceeding those of other methods, demonstrating the potential use of RT-QuIC as an early diagnostic test. The reliability of this quantitative, highly sensitive and specific RT-QuIC assay for proteinopathies could help us in understanding the mechanisms of diseases as well as in determining the efficacy of potential disease modifying therapies.