Yes, you can have a virus for that long. With all that you've described I'd guess that you don't have lupus. You are missing most of the symptoms that would be required for the diagnosis of it.
People can have a positive ANA w/o having lupus. A virus or being sick can cause that. I notice you mention you back and the pain above your knees and elbows, it's possible that you may have Fibro. I'm by no means a doctor and can't say that you do have it.
I do know though I have RA/Lupus/Fibro and low grade temps can be common in folks with Fibro too. As well as the muscle pain. With lupus our joint really hurt and can swell a lot. I'd go back and see the Dr and see what they have to say.
My daughter has had a positive ANA since was like 8, she's now 20 and she still hasn't developed lupus or any other auto immune disease. Try not to worry to much I think you should talk with Dr and see if you both can figure things out.
Good luck and let us know how it goes.
DX- RA, Lupus, Fibro, LGL Leukemia, Pulmonary Hypertension, Bells Palsy, Gastroparsis, Blood Clots, Cateracts, Glaucoma, Chronic Pericarditis & Pleurisy, Severe Anemia. Way to many medications to list.