Results
We prospectively enrolled 19 subjects with severe COVID-19 related pneumonia who required endotracheal intubation and mechanical ventilation for acute hypoxemic respiratory failure between Aug 2020 and March 2021 when the alpha variant was in widespread circulation. One subject was prospectively enrolled into a separate study in May 2020 and his BAL sample and plasma samples were available for use in future studies. All subjects had positive nasopharyngeal SARS-CoV-2 RT-PCR and two subjects had negative viral RT-PCRs on evaluation of the bronchoalveolar lavage (BAL). The 18 subjects with positive BAL had a mean age of 68 years (SD 7.8 years) and were predominantly white (83.3%) (Table 1 and supplemental Table E1). Males and females were equally distributed. 33.3% (6 of 20) of subjects were considered immunocompromised: three were solid organ transplant recipients and three suffered from rheumatologic conditions. Chronic immunosuppressive medications in these six subjects included mycophenolic acid, prednisone, tacrolimus, sirolimus and azathioprine. Subjects underwent bronchoscopy 3.6 days (SD 3.6 days) after intubation and 13.7 (SD 7.8) days after development of symptoms (3 subjects in week 1, 7 in week 2, 6 in week 3 and 2 in week 5). All eighteen subjects received corticosteroids prior to bronchoscopy, 17/18 received remdesivir and
one subject received tocilizumab 8 days prior to the BAL. Mortality was 55.6% with 1.8 average ventilator free days (SD 2.9 days).
Survivors and non-survivors had similar age and immuncompromising comorbidities. The majority of non-survivors were admitted from outside hospitals and had a longer duration of intubation.