Chronic Lyme Disease: This condition, caused by the bacterium Borrelia burgdorferi, often presents with prolonged low-grade fever, joint pain (especially in the knees), and can have a variety of other symptoms including fatigue and neurological issues. The chronic nature of the symptoms and the specific mention of joint pain make this a strong consideration.

Rheumatoid Arthritis (RA): An autoimmune disorder that causes chronic inflammation and pain in the joints. It can also be associated with low-grade fever, especially during active disease phases. The joint pain in RA is typically symmetric and can lead to significant disability if not treated.
Osteoarthritis (OA): While OA is more commonly associated with wear and tear on the joints and less likely to cause systemic symptoms like fever, some forms, especially when complicated by infections or significant inflammation, could present with low-grade fever and joint pain.
Fibromyalgia: A long-term condition characterized by widespread pain in the muscles and bones, areas of tenderness, and general fatigue. Some patients may also experience low-grade fever, though this is less common.

Tuberculosis (TB): A bacterial infection that can affect various parts of the body, including the lungs, kidneys, and spine. It often presents with chronic symptoms such as low-grade fever, weight loss, and night sweats. Joint pain can occur if the infection involves the skeletal system. Missing TB can lead to severe consequences, including death.
Endocarditis: An infection of the inner lining of the heart chambers and valves. It can cause prolonged fever, joint pain, and other systemic symptoms. This condition is life-threatening and requires prompt diagnosis and treatment.
Lymphoma: A type of cancer that begins in cells of the lymph system. Some forms can present with prolonged low-grade fever, joint pain, and other systemic symptoms like weight loss and night sweats. Early diagnosis is crucial for effective treatment.

Relapsing Polychondritis: A rare autoimmune disorder characterized by recurring episodes of cartilage inflammation. It can affect various types of cartilage in the body, including that found in the ears, nose, trachea, and joints, and may present with fever and joint pain among other symptoms.
Whipple's Disease: A rare, systemic bacterial infection caused by Tropheryma whipplei. It can lead to malabsorption, weight loss, joint pain, and fever, among other symptoms. The disease is rare but can be fatal if not treated.
Adult-Onset Still's Disease: A rare inflammatory disorder that can cause high fevers, joint pain, and swelling, among other symptoms. It's an autoimmune condition that can mimic other diseases, making diagnosis challenging.