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Additional file 1: Figure S1. Maximum level of oxygenation support during the index hospitalization for patients who experienced treatment failure. IV: invasive mechanical ventilation; HFC: high flow nasal cannula; NIV: non-invasive ventilation.

Additional file 4: Figure S4. Adjusted risk difference and adjusted odds ratio (OR) for treatment failure for each risk factor from a conservative imputation model. In this model, we included only patients with confirmed dates for both SARS-CoV-2 positive test and mAb administration. Risk differences were calculated via Firth's bias-reduced multiple regression logistic regression. Adjusted ORs and 95% confidence intervals (95% CI) were computed by penalized profile likelihood.

Background: Detailed understanding of the immune response to severe acute respiratory syndrome coronavirus (SARS-CoV)-2, the cause of coronavirus disease 2019 (CO­VID-19) has been hampered by a lack of quantitative antibody assays. Objective: The objective was to develop a quantitative assay for IgG to SARS-CoV-2 proteins that could be implemented in clinical and research laboratories. Methods: The biotin-streptavidin technique was used to conjugate SARS-CoV-2 spike receptor-binding domain (RBD) or nucleocapsid protein to the solid phase of the ImmunoCAP. Plasma and serum samples from patients hospitalized with COVID-19 (n = 60) and samples from donors banked before the emergence of COVID-19 (n = 109) were used in the assay. SARS-CoV-2 IgG levels were followed longitudinally in a subset of samples and were related to total IgG and IgG to reference antigens using an ImmunoCAP 250 platform. Results: At a cutoff of 2.5 μg/mL, the assay demonstrated sensitivity and specificity exceeding 95% for IgG to both SARS-CoV-2 proteins. Among 36 patients evaluated in a post-hospital follow-up clinic, median levels of IgG to spike-RBD and nucleocapsid were 34.7 μg/mL (IQR 18–52) and 24.5 μg/mL (IQR 9–59), respectively. Among 17 patients with longitudinal samples, there was a wide variation in the magnitude of IgG responses, but generally the response to spike-RBD and to nucleocapsid occurred in parallel, with peak levels approaching 100 μg/mL, or 1% of total IgG. Conclusions: We have described a quantitative assay to measure IgG to SARS-CoV-2 that could be used in clinical and research laboratories and implemented at scale. The assay can easily be adapted to measure IgG to mutated COVID-19 proteins, has good performance characteristics, and has a readout in standardized units.

Study Design: 30 subjects with CF were enrolled in the study. Study visits were performed at quarterly CF visits and at the time of an exacerbation over a two-year period. At each study visit, subjects underwent a history, physical, medication history and a culture obtained by oropharyngeal (OP) swab. Chest radiographs were done at study enrollment and at study completion (2Â years) during periods of clinical stability and assigned a Brasfield score. (JPEG 27Â kb)

Additional file 8: Table S6. Cycle threshold values for nucleocapsid and RNase P genes from simulated shipping data. Saliva samples were spiked at 50 and 12 SARS CoV-2 copies/��L, then processed fresh, with the summer or winter profiles.

Background: Acute kidney injury (AKI) is a well-recognized complication of coronavirus disease 2019 (COVID-19). The short and long-term outcomes of patients who develop AKI have not been well characterized. Methods: In this multicenter retrospective cohort study, we describe the clinical characteristics and outcomes of critically ill adults with severe COVID-19 and AKI. Patient-level variables were extracted from the electronic medical record. Using nadir-to-peak serum creatinine, AKI was defined using the KDIGO definition. Multivariable logistic regression analyses examined factors associated with development of moderate-to-severe (stage 2–3) AKI, severe (stage-3) AKI, and the composite of renal replacement therapy (RRT) or in-hospital death. Results: Among 459 critically ill adults with COVID-19, 371 (80.1%) developed AKI, with 179 (37.9%) developing stage-3 AKI. Male gender, black and Asian/Native American race, lower baseline estimated glomerular filtration rate (eGFR), higher body mass index (BMI), and higher Acute Physiology and Chronic Health Evaluation (APACHE) IV score were more prevalent among patients with severe AKI, as were systemic markers of inflammation. On multivariable analysis, male gender, black and Asian/Native American race, higher APACHE IV score, lower baseline eGFR, and higher BMI (mainly the highest BMI stratum ≥35 kg/m2) were independently associated with higher stages of AKI severity. Male gender, lower baseline eGFR, and higher APACHE IV score were also independently associated with the composite of RRT or in-hospital death. Moderate-to-severe AKI and severe AKI were independently associated with in-hospital death, and there was a significant interaction between BMI and moderate-to-severe AKI for the outcome of in-hospital death. Among 83 (18.1%) patients who required RRT, 27 (32.5%) survived, and 12 (44.4%) remained dialysis-dependent at discharge. At 3 and 6 months, 5 (41.7%) and 4 (33.3%) remained dialysis-dependent, respectively. Conclusions: AKI is common in critically ill adults with COVID-19. Several patient-level risk factors are associated with higher stages of AKI severity. BMI might be an effect modifier of AKI severity for in-hospital death. Among AKI survivors, there is a high rate of short- and long-term dialysis dependence.

Additional file 4: Supplemental Table 3. Protein Ontology representation of SARS-CoV-2 proteins. Comparative information in RefSeq and UniProtKB is also provided.

Additional file 4: Supplemental Table 3. Protein Ontology representation of SARS-CoV-2 proteins. Comparative information in RefSeq and UniProtKB is also provided.

Additional file 7: Table S2. Internal reliability for survey questions. The majority of internally reliable survey questions did not differ significantly across collection devices. (a) Analysis of responses for participant and observer survey questions found to be internally reliable with Cronbach���s alpha. (b) Analysis of laboratory survey responses.