The APS Phenotyping Study

"Blood will be collected from a catheter (IV) that is already in place or using a needle stick into a vein.~Blood will be collected in hospital (Cohorts A, B) and at visits 3, 6, and 12 months following hospitalization for (Long-term Outcomes Cohort)."

"Urine will be collected through a urinary catheter that is already in place or by urinating into a cup.~Urine will be collected in hospital only (Cohorts A, B)"

"Nasal, oral, and rectal swabs inserted into the nose, mouth, and rectum, respectively. The swabs will be rubbed inside the cavity and then removed the swab.~Oral and nasal swabs will also be collected in hospital (Cohort A, B) and at visits 3, 6, and 12 months following hospitalization for (Long-term Outcomes Cohort). Rectal swabs will be collected in hospital only (Cohorts A, B)."

"Stool will be collected either in a cup after defecation or by collecting it from a tube or bag that may already be in place that is catching stool.~Stool will be collected in hospital (Cohorts A, B) and at visits 3, 6, and 12 months following hospitalization (Long Term Outcomes Cohort)."

"An HME filter is a sponge that is placed in the tubing between a patient and breathing machine. It reduces the amount of heat and moisture a patient loses when on a breathing machine. Moisture from breath is collected in this filter. The filter is changed every few hours. When the filter is changed, it will be saved to collect the moisture that it contains and run tests on it.~HME filters will be collected in hospital on intubated patients only (Cohorts A, B)."

"Patients on a breathing machine have a breathing tube in their trachea that connects their lungs to the breathing machine. A smaller tube, called a suction catheter, will be placed through the larger tube and fluid will be gently sucked out.~Tracheal aspirate will be collected in hospital on intubated patients only (Cohorts A, B)"

"The NBBAL procedure involves putting a flexible rubber tube through the breathing tube into the airway of one of the lungs. A small amount of fluid is injected into the lung and then a gentle suction is used to collect fluid. Only patients who pass a safety screen showing that they are not at high risk for complications will have the NBBAL procedure performed.~NBBAL will be performed in hospital on intubated patients only (Cohort A)"

Participants will be contacted by email, text, and /or phone to give updates about their health. These surveys will ask questions about quality of life, mental health, return to work, and re-admission to the hospital. (Cohort A)

"At visits 3, 6, and 12 months following hospitalization (Long-term Outcomes Cohort)~Chair Stand Test: For this test the participant will sit in a chair. They will then stand as quickly as possible without using their upper body to assist them.~Balance Test: For this test the participant will stand unsupported for 10 seconds with their feet in 3 different positions.~4-meter walk: For this test the participant will walk 4 meters as quickly as possible."

"At visits 3, 6, and 12 months following hospitalization (Long-term Outcomes Cohort):~The participant will squeeze a machine called a hand-held dynamometer 3 times with all their strength."

"At visits 3, 6, and 12 months following hospitalization (Cohort A - Long-term Outcomes Cohort):~The participant will sit at a computer and follow the prompts on the screen. This test takes about 45 minutes."

"At visits 3, 6, and 12 months following hospitalization (Long-term Outcomes Cohort):~The participant will undergo ultrasound on the quadriceps muscle on the dominant side of their body."

"At visits 3, 6, and 12 months following hospitalization (Long-term Outcomes Cohort):~A dynamometer will be used to measure muscle strength in the dominant leg."

"At a visit 12 months following hospitalization (Long-term Outcomes Cohort):~The participant will have a clip placed on their nose and will be given a plastic mouthpiece that is connected to a machine called a spirometer. They will place their lips tightly around the mouthpiece and take in as big and deep of a breath as possible and then blow out as hard and fast as they can."

"At a visit 12 months following hospitalization (Long-term Outcomes Cohort):~The participant will have a clip on their nose. They will put their mouth over a mouthpiece that is attached to a machine. This machine will deliver a small amount of carbon dioxide when they breathe in and will also record the results of the test. They will then take a few normal breaths. Next they will inhale deeply and exhale completely. They will breathe in quickly through their mouth and hold their breath for 10 seconds or as long as they can. Then they will breathe out."

"At a visit 12 months following hospitalization (Long-term Outcomes Cohort):~The participant will undergo a Chest Computed Tomography (CT) scan which uses special X-ray equipment to take detailed pictures of the lungs."