Primary care providers are often the first to evaluate patients with unexplained breathing problems. Shortness of breath, fatigue and a lingering cough are all common complaints that frequently point to asthma, COPD or recurrent pneumonia. But in some cases, these symptoms can be a sign of something much rarer, for example, autoimmune pulmonary alveolar proteinosis (aPAP).
“aPAP is a rare lung condition that can be difficult to diagnose because it may mimic many other more common lung diseases,” explains Dr. Ali Ataya, pulmonologist and rare lung disease specialist. “Patients are often told they have asthma or recurrent pneumonia and that can delay getting the right treatment, especially early in the course of this disease."
Understanding aPAP
In healthy lungs, a naturally forming substance called surfactant coats the inside of the air sacs, keeping them open and allowing oxygen to pass into the bloodstream. In people with autoimmune PAP, the body does not clear surfactant efficiently and it begins to build up in the lungs. Over time, this buildup makes it harder for oxygen to move into the blood and leads to worsening symptoms.
Initially, people living with aPAP may not have any symptoms. However, patients will usually end up experiencing shortness of breath that often gets worse with activity. Fatigue is common, as is a chronic cough. Because these symptoms overlap with so many other lung conditions, aPAP can remain undiagnosed for months or even years.
Recognizing the Red Flags
For primary care providers, one of the most important clues is when symptoms do not improve with standard treatments. Patients may be treated repeatedly for pneumonia without full resolution, or they may continue to struggle with breathing problems despite using inhalers for presumed asthma. It’s important for a provider to determine if there are resolvable barriers to using the medication, such as cost or technique, that might be getting in the way of the optimal treatment outcome. But sometimes, the reason patients aren’t getting better is because they don’t have the disease they have been diagnosed with.
“That’s why seeing a specialist matters,” said Dr. Ataya. “Healthcare providers with experience managing a variety of rare lung conditions will be familiar with aPAP and will know to look for specific signs and order the right tests.”
Specialists may order a chest CT scan, which can show hazy areas in the lungs that create a distinctive “crazy paving” pattern. More importantly, a blood test is now also available to confirm the diagnosis by detecting GM-CSF autoantibodies, which are specific to aPAP. “The commercial availability of the GM-CSF autoantibody test, which can be a simple blood draw or finger-prick blood test, has made it much simpler to test and diagnose patients quickly and accurately, early in the course of this disease.” Dr. Ataya continues "It helps avoid more invasive lung biopsy testing in many patients.”
Why Early, Accurate Diagnosis Matters
Catching aPAP early is critical to avoid unnecessary treatments and get patients on the right path. Once diagnosed, most people can manage the disease well under the guidance of a pulmonologist and a personalized treatment plan.
“Recognizing these signs early can make all the difference in getting the right treatment and avoiding unnecessary delays and more invasive procedures and treatments” Dr. Ataya emphasizes.
Moving Forward
For primary care providers, keeping aPAP in mind when a patient has unexplained, persistent lung symptoms can change the trajectory of care. If a patient is not improving as expected, consider ordering the GMCSF autoantibody test and referral to a pulmonologist or rare lung disease specialist. If you are a patient with unresolved respiratory symptoms, ask your healthcare provider about seeing a specialist to rule out a rare lung disease.
Educational content developed with support from Savara, Inc.
Blog last updated: October 27, 2025
