Both your mood and your processing of pain are affected by chemicals in your brain called neurotransmitters, in this case serotonin and norepinephrine. So big swings in mood can also affect how you handle pain.
Taking antidepressants which block one of those chemicals can also give you physical symptoms as a side effect for the same reason.
Those aches, pains, and stomachache might have already been there, but were so minor the brain tuned them out like it does with background noise–it wasn’t important. But with its handling of pain mixed up, that pain isn’t hidden anymore. People’s bodies often just ache a tiny bit all the time from the basics of daily life, after all.
Or the pain might be indirectly caused by behavior during depressive episodes, like bad posture or resting body position creating aches and joint pain, or anxiety or bad diet stirring up indigestion. This is why depression is complicated, and it’s physical symptoms can come and go or last after the episodes, be treated with a painkiller one day and not another. Sometimes it’s all in the brain, and sometimes it’s new, physical issues.
Physical symptoms with these issues are sometimes a sign of depression in those who aren’t yet diagnosed, since they’ll see a doctor about their pain only, often unaware of the true cause and never bringing up the depression.
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