Causes of long term Lyme disease symptoms
Multiple studies have shown that as many as 34% to 62% of patients have Lyme disease symptoms that persist long term despite treatment. [1,2] These patients can suffer for years with debilitating symptoms.
Long term lyme disease symptoms are all to common. According to one study, at their six-month follow-up visit, “36% of patients reported new-onset fatigue, 20% widespread pain, and 45% neurocognitive difficulties.” 
So, how could Lyme disease symptoms persist long term? There have been many theories, including recent findings that suggest persistent symptoms may be due to antigenic variation.A new study reports that antigenic variation may explain why some Lyme disease patients continue to have chronic symptoms. Click To Tweet
In their article “Changing of the guard: How the Lyme disease spirochete subverts the host immune response,” Chaconas and colleagues  explain how antigens, or proteins on the surface of the spirochetal bacteria, play a sort of “cat and mouse” game with the immune system.
Other pathogens use antigen variation
Antigen variation is not unique to Lyme disease, Chaconas writes. Rather, it’s a “common pathogenic ruse employed by several bacterial, protozoan, and fungal pathogens.”
In fact, “Many bacterial and protozoal pathogens have developed antigenic variation systems in which surface antigens can be continually altered as a means of evading the constant onslaught of adaptive antibody and T cell responses,” Chaconas writes.
The immune system is designed to recognize these antigens and kill the spirochete. But, the spirochetal bacteria can change these antigens, thereby evading the immune system’s attack.
“This process involves changes in a prominent surface antigen such that it is no longer recognized by the host acquired immune response,” Chaconas writes.
Altering the immune response
By changing the antigens, the spirochetes buy time. This may explain why Lyme disease symptoms continue long term in some individuals. As the authors explain, “By the time the host has assembled and produced antibodies to clear an infecting organism, new variants have appeared, which fly under the radar in terms of immune surveillance.”
The process is like a cat-and-mouse game, “which can often continue for the long haul, resulting in persistent infection by pathogenic organisms, and provides an efficient mechanism whereby they can avoid clearance by the host immune system.”
Spirochetes buy even more time by changing the antigens yet again. “By the time a new generation of antibody molecules has been fashioned to clear the variant pathogens, yet another collection of organisms with prominent but unrecognizable surface antigens has appeared,” the authors write.
Vls gene responsible for antigenic variation
The gene vls locus enables antigenic variation.
“The vls system is required for long-term survival of Lyme Borrelia in infected mammals and represents an important mechanism of immune evasion,” writes Norris in Microbiology Spectrum. 
“The vls locus is akin to a perpetual motion machine for antigenic variation in Lyme Borrelia species,” Norris writes.
Authors conclude: Additional studies are needed to examine vls locus, given there have been reports of persistent infections in treated animals.
“If there is a link, then the development of a drug blocking recombinational switching at vlsE would offer a promising response to drug-surviving spirochetes and would provide a direct block to the development of long-term persistence.”
Persistent Lyme infection or inflammatory immune response?
Is suppressing the immune system harmful to Lyme patients?
- Shadick NA, Phillips CB, Logigian EL, et al. The long-term clinical outcomes of Lyme disease. A population-based retrospective cohort study. Ann Intern Med. 1994;121(8):560-567.
- Asch ES, Bujak DI, Weiss M, Peterson MG, Weinstein A. Lyme disease: an infectious and postinfectious syndrome. J Rheumatol. 1994;21(3):454-461.
- Aucott JN, Rebman AW, Crowder LA, Kortte KB. Post-treatment Lyme disease syndrome symptomatology and the impact on life functioning: is there something here? Qual Life Res, 22(1), 75-84 (2013).
- Chaconas G, Castellanos M, Verhey TB. Changing of the guard: How the Lyme disease spirochete subverts the host immune response. J Biol Chem. 2020 Jan 10;295(2):301-313.
- Norris SJ. vls Antigenic Variation Systems of Lyme Disease Borrelia: Eluding Host Immunity through both Random, Segmental Gene Conversion and Framework Heterogeneity. Microbiol Spectr. 2014 Dec;2(6).
I had a long-time, undiagnosed bout with Lyme (about 2 years) before finally showing up in bloodwork. Another 2+ years of antibiotics which did not knock down my infection until I had a Pic-line installed in my arm which enabled me to self-inject liquid antibiotics directly into my heart. I developed congestive heart failure, had 2 sets of stents (4 total) inserted in my coronary arteries, and finally underwent an aortic valve replacement in 2019. I continue to suffer from severe muscle spasms in legs and arms, sporadic crippling spasms in my hands and feet, and recurring bouts of “Tickling Itching” in my extremities which is un-relentless & debilitating usually lasting 3 to 5 days before subsiding. Blood test results have indicated that the presence of Lyme falls short of the State mandated benchmark for treatment. I am a Type 2 Diabetic, have had by-pass surgery and suffer from neck issues.
I find it a challenge when my patient has more than one condition. I have to address each condition concurrently.
I seriously cannot find ANY doctors in the Pittsburgh area who believe in this. We have great doctors! I have been sick since 1990. They diagnosed it as CFS. I didn’t have a rash, just symptoms. In 2016, Infectious Disease said that I most likely had it at once point. At that point, the test had just one reactive marker. I would love to not get shocked anymore….
I have had to use clinical judgement when there is only one band. There must have been something the ID was looking at. There is no test to be sure Lyme disease had resolved.
Hello, I began reading your blog a few months and have learned a lot. My interest is because I have untreated chronic Lyme. I believe I contracted Lyme as soon as I moved back to upstate new york. In late 2015 I had what I call “my initial attack” , where I thought I was going to die.although I was an avid fisherman, rock climber and repeller, the doctors had everything wrong. They tested me for everything except Lyme, this even included a left leg muscle biopsy, neurologic problems which led my neurologist stated that in her opinion, I’ve had numerous Lyme infections, Lyme meningitis and Lyme carditis . Long story semi short, I go through horrible flareups and suffer from advanced arthritis, chest pains, left leg is week and unstable and much more. How, and where, could I see a Lyme specialist?
Call the office at 914 666 4665. You could also contact Global Lyme Alliance or Lyme disease association for names.