First things first. What is a pathogen? A pathogen is a generic term for anything that can cause disease. Pathogens are often sub categorized as viruses, bacteria, fungi, parasites, and prions. Each of these subcategories of pathogens have been known to cause disease in humans. Many pathogens are well documented, have known means of identification, and have known means of treatment. However, for every well-known pathogen, there are many more unknown pathogens with unknown symptoms and outcomes.
Two case-in-points: Lyme Disease and Hantavirus.
Lyme Disease wasn't identified until the early 1970s when an affluent community in Connecticut experienced a wide-reaching epidemic of unknown and debilitating illness (preliminarily identified as rheumatoid arthritis). The episode garnered the interest of researchers and universities and resources were devoted to finding the cause. It wasn't until 1982 (almost a decade) until the bacteria that caused the unknown illness was identified. The reason it took so long was because the bacteria, a spirochete, was really good at hiding in the body and very difficult to find via conventional diagnostic tools. Click here for an article on the discovery of Lyme's Disease by the Connecticut Department of Public Health. Hantavirus, a respiratory illness, was first identified by the modern medical community in the early 1990s after several fatalities from an unknown illness in the four corners region of the southwest spurred interest in the disease. Click here for an article on the discovery of the disease by the CDC. Hantavirus and Lyme Disease existed before they were documented by the modern scientific community; however, if you would have visited a doctor with these diseases prior to identification they would have been misdiagnosed and you would not have received effective treatment.
Both Lyme Disease and Hantavirus have devastating outcomes - debilitating chronic disease and/or death, which is one of the reasons why they garnered so much attention from the medical community. Imagine with me, if you will, a scenario where the outcome of an budding but unknown disease or diseases is mild and generic chronic illness. Would anyone be interested in or put money towards finding out the source of this illness? Fortunately, the answer to that question is yes. There are doctors and institutions looking for a pathogenic source for chronic illness (click here to read a few blogs on the subject). Okay, now imagine with me that this pathogenic source is extremely good at hiding in the body, similar to Lyme disease. Will it (or they) ever be found? Good question - only knowable if someone finds one or more pathogens that can be associated with mild chronic symptoms. The bottom line is that one (or multiple) currently unknown pathogens could be responsible for one or more chronic diseases.
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