Human herpesvirus 6 or HHV-6, is a herpes virus just like Epstein-Barr Virus, Cytomegalovirus, Chicken pox (varicella zoster), HHV-7, HHV-8 and Herpes simplex 1 and 2.  There are two types of this virus including HHV-6A and HHV-6B. 100% of human beings get infected with HHV-6B by the age of three which results in fever, diarrhea and a rash called roseola. In rare cases it can cause seizures and encephalitis.  There are many infection connections to autoimmune diseases like Hashimoto's disease and in this article I'll cover the connection between HHV-6 and Hashimoto's disease.

Less is known about HHV-6A which was found in a small study in 50% of adults.  HHV-6A is said to be the most problematic of the two types and it is the type found inside the thyroid glands of some people with Hashimoto’s thyroiditis.

Just like other herpes viruses, HHV-6 can reactivate (occurs in the thyroid gland, GI tract, brain, heart, kidneys, uterus, and lungs) later in life when the immune system is compromised resulting in a variety of conditions including:

Hashimoto’s thyroiditis
Sjogren's syndrome
Lupus
Rheumatoid arthritis
Sarcoidosis
Guillan-Barre
Multiple Sclerosis
Infertility
Chronic fatigue syndrome
Fibromyalgia
HIV progression to AIDS
Epilepsy
Seizures
Immune suppression
Certain types of cancer
Kidney, liver, lung disease
Heart disease
Encephalitis
Colitis
Transplant recipient issues
Bone marrow suppression
Autoimmune hepatitis
What is the link between HHV-6 and Hashimoto’s disease?
Here are some studies supporting the connection between HHV-6 and Hashimoto's disease:

Rizzo et al. in 2016 found a direct connection among natural killer cell activation, thyroid antibodies, and HHV-6 in patients with Hashimoto's disease.  This study found that the HHV-6 virus causes an increase in natural killer cells against the virus which causes an ongoing inflammatory process in the thyroid gland that correlates with thyroid peroxidase and anti-thyroglobulin antibodies.  This means that an active HHV-6 infection in the thyroid gland drives the elevation of thyroid antibodies and increases inflammation in the gland resulting in increased damage to thyroid tissue.

A study published in 2012 entitled "Virologic and Immunologic Evidence Supporting an Association between HHV-6 and Hashimoto's Thyroiditis" by Caselli et al. found that a high percentage of patients in the study with Hashimoto’s disease have active HHV-6A infections inside the thyroid gland.  This increases inflammation in the thyroid gland since the immune system is concerned about Human herpesvirus 6 and due to antibodies against the thyroid gland.

A follow-up study by Caselli et al. in 2017 entitled "HHV-6A in vitro infection of thyrocytes and T cells alters the expression of miRNA associated to autoimmune thyroiditis" also found a connection between HHV-6 and Hashimoto's disease.

Sultanova et al. in their 2017 paper entitled