Hashimoto's looks like an autoimmune cross-targeting triggered disease

Autoimmune cross-targeting hypothesis: a virus marks the inside of a cell while a larger infection marks the outside and the combination triggers autoimmune disease.  The immune system is instructed to destroy both the inside and the outside of the target.

Multiple viruses can trigger Hashimoto's  but it only takes one to mark the inside while a fungal infection or mycoplasmas mark the outside.

Epstein barr virus has been found in Hashimoto's
http://www.ncbi.nlm.nih.gov/pubmed/25931043

parvovirus B15 has been found in Hashimoto's
http://www.ncbi.nlm.nih.gov/pubmed/18788945

Flaviviruses like dengue can infect the thyroid and could trigger Hashimoto's too
http://bmcinfectdis.biomedcentral.com/articles/10.1186/1471-2334-12-240

west nile infects the thyroids of birds
http://www.ncbi.nlm.nih.gov/pubmed/19432016

Hepatitis C (a flavivirus )has been found
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2350409/
http://www.ncbi.nlm.nih.gov/pubmed/1342367

HTLV-1 has been found in Hashimoto's
http://www.ncbi.nlm.nih.gov/pubmed/1460458
http://www.ncbi.nlm.nih.gov/pubmed/1843058

Hashimoto's and fungal infections: It is unclear how fungal infections are triggering the peroxidase antibodies which cause the targeting of the thyroid.  How this happens must still be solved.  Perhaps our body's immune system starts to associate the peroxide we fight infections as foreign? Do fungal infections attempt to modify peroxidase or make their own peroxidases?

Family with genetic disorder linking Hashimoto's and Candida infections

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1226065/

Sjogren's with Hashimoto's  thyroid
http://www.ncbi.nlm.nih.gov/pubmed/23884987
http://www.ncbi.nlm.nih.gov/pubmed/16984944
http://www.ncbi.nlm.nih.gov/pubmed/8422556
http://www.ncbi.nlm.nih.gov/pubmed/9010968

Candida and Sjogren's
http://www.ncbi.nlm.nih.gov/pubmed/9343767
http://www.ncbi.nlm.nih.gov/pubmed/10200720

aspergillus niger makes peroxidases
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC92105/

Graves becomes hashimoto's in 20% of patients on antithyroid treatment
http://www.ncbi.nlm.nih.gov/pubmed/2434520

The reason for this is that the drug replaces the virus in triggering an autoimmune cross-targeting reaction.  With the mycoplasmas marking the outside of the thyroid. (the receptors binding antibodies are internalized too quickly)


 thyroid peroxidase (TPO) (also called TPOAb) and/or thyroglobulin