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Swollen Lymph Nodes/Enlarged Thyroid, Normal Ultrasound??

I was diagnosed as Subclinical Hypothyroidism in April of 2016, and placed on a dose of 25 mcg Levothyroxine once per day.  This worked well until June of 2016 - I came down with a sore throat, swollen uvula and have gotten progressively sicker ever since.  I'm still losing my hair by the handful, having trouble falling (and staying) asleep, have pressure in my throat, feeling like someone has their hands around my throat and are choking me.    My doctor said my tonsils were swollen, she felt swollen lymph nodes and my thyroid was enlarged.  My TSH is 2.36, free T4 is 1.31.   A mono screening was ran and came back negative.  A Blood Panel was ran and everything came back within normal limits.     She sent me for an ultrasound that came back clean, no nodules or anything.

What the heck is going on? Is it possible that the ultrasound was wrong?  If I had some sort of infection that were causing the swollen lymph nodes/enlarged thyroid, wouldn't the CBC have shown that?
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A starting dose of 25 mcg of T4 usually accomplishes nothing.  The reason is that the med will cause the TSH to go down and that results in less production of natural thyroid hormone.  Since serum thyroid levels are the sum of both natural thyroid and thyroid med, the level may not increase at all until the TSH is diminished to a low enough level that it no longer stimulates the thyroid gland,  At that point, further increases in thyroid med will cause an increase in Free T4 and Free T3 levels.  

At this point there is insufficient evidence that your hypothyroidism is the sole cause for your symptoms.  You need to always test for both Free T4 and Free T3 every time you go for tests.  Free T3 is the thyroid hormone that affects all the cells in your body and it correlates best with hypothyroid symptoms.  In addition, hypo patients are frequently too low in the ranges for Vitamin D, B12 and ferritin, so you need to test those and then supplement as needed to optimize.  D should about 50 min., B12 in the upper end of the range, and ferritin should be 70 min.  

Two other tests I suggest are cortisol and Reverse T3 (with a Free T3 done from the same blood draw).

If you are able to get those done, then post results here and we will be happy to help interpret and advise further.  

Be aware that a good thyroid doctor will treat a hypothyroid patient clinically by testing and adjusting Free T4 and Free T3 as needed to relieve symptoms, without being constrained by resultant TSH levels.  Symptom relief should be all important, not just test results.  
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