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Archaeal endosymbiosis leads to selenium deficiency. The archaea uses selenium to synthesize archaeal selenoproteins. This leads to cellular selenium deficiency. Selenium deficiency leads to defective retroviral propagation as the retroviruses contain selenoprotein sequences and need selenium to synthesize them. Selenium deficiency leads to defective glutathione synthetase and glutathione peroxidase dysfunction leading to free radical stress and neurodegeneration, cancer, autoimmune disease and metabolic syndrome. Selenium deficiency leads to defective T4 to T3 conversion as deiodinase needs selenium as a cofactor. Selenium deficiency leads to hypothyroidism and Hashimoto's thyroiditis. Selenium deficiency leads to cardiomyopathy and pancreatitis. Hashimoto's thyroiditis consequent to selenium deficiency is associated with cerebral small vessel disease, normal pressure hydrocephalus, Hashimoto's encephalopathy, non-vasculitic autoimmune meningitis, autoimmune dementia and recurrent hyponatraemic encephalopathy. Selenium deficiency leads to an endocrine cardiac syndrome and a neurological syndrome.