Extended Data Table 1.
Clinical characteristics of patients infected with SARS-CoV-2 based on viral genotype
| Clinical Characteristic | E484K (n=170)1 | Wildtype1 (n=1,180) | P2 | B.1.526-E484K1 (n=232) | Non-VOI/VOC lineages1 (n=790) | P2 |
|---|---|---|---|---|---|---|
| Demographics | ||||||
| Male sex, n (%) | 80 (47.1) | 539 (45.7) | 0.806 | 97 (41.8) | 373 (47.3) | 0.159 |
| Age, years (median [IQR]) | 56 [36, 68] | 55 [33, 70] | 0.9653 | 51 [32, 69] | 51 [30, 68] | 0.7433 |
| Race and ethnicity, n (%) | 0.288 | 0.117 | ||||
| Hispanic/Latino | 87 (51.2) | 548 (46.5) | 122 (52.6) | 357 (45.3) | ||
| Black | 11 (6.5) | 131 (11.1) | 27 (11.6) | 89 (11.3) | ||
| White | 24 (14.1) | 172 (14.6) | 23 (9.9) | 119 (15.1) | ||
| Other | 48 (28.2) | 328 (27.8) | 60 (25.9) | 223 (28.3) | ||
| Place of residence, n (%) | 0.008 | 0.002 | ||||
| NYC | 151 (88.8) | 959 (81.3) | 204 (87.9) | 627 (79.4) | ||
| Yonkers | 7 (4.1) | 34 (2.9) | 9 (3.9) | 23 (2.9) | ||
| Outside NYC and Yonkers | 12 (7.1) | 187 (15.8) | 19 (8.2) | 140 (17.7) | ||
| Comorbidities | ||||||
| BMI, kg/m2 (median [IQR]) | 28.9 [25.0, 33.1] | 27.1 [23.5, 31.3] | 0.013 | 28.6 [24.7, 33.1] | 26.6 [23.1, 30.5] | 0.0013 |
| Hypertension, n (%) | 70 (41.7) | 444 (41.2) | 0.981 | 86 (38.4) | 291 (40.6) | 0.602 |
| Diabetes mellitus, n (%) | 51 (30.4) | 265 (24.6) | 0.134 | 63 (28.1) | 166 (23.2) | 0.157 |
| Chronic kidney disease, n (%) | 21 (12.5) | 126 (11.7) | 0.864 | 18 (8.0) | 93 (13.0) | 0.059 |
| Coronary artery disease, n (%) | 13 (7.7) | 108 (10.0) | 0.428 | 16 (7.1) | 72 (10.1) | 0.240 |
| Solid organ transplant, n (%) | 7 (4.2) | 42 (3.9) | 1.00 | 7 (3.1) | 41 (5.7) | 0.171 |
| Cycle threshold value (mean (SD)) 4 | 29.49 (5.64) | 30.71 (5.66) | 0.013 | 27.65 (4.88) | 28.81 (4.93) | 0.015 |
| Severity of care and outcomes | ||||||
| Highest level of care, n (%) | 0.175 | 0.037 | ||||
| Admitted | 50 (29.6) | 417 (35.4) | 81 (35.1) | 228 (29.0) | ||
| Emergency Department | 64 (37.9) | 339 (28.8) | 83 (35.9) | 243 (31.0) | ||
| ICU | 13 (7.7) | 86 (7.3) | 15 (6.5) | 54 (6.9) | ||
| Outpatient | 42 (24.9) | 335 (28.4) | 52 (22.5) | 259 (33.0) | ||
| Supplemental oxygen, n (%) | 48 (85.7) | 348 (77.5) | 0.217 | 67 (81.7) | 187 (73.9) | 0.199 |
| Outcome, n (%) | 0.454 | 0.565 | ||||
| Deceased or discharged to hospice | 8 (4.7) | 87 (7.4) | 10 (4.4) | 45 (5.7) | ||
| Further care at external facility | 16 (9.5) | 85 (7.2) | 16 (7.0) | 44 (5.6) | ||
| Discharged to home | 145 (85.8) | 1003 (85.4) | 202 (88.2) | 693 (88.5) |
Wildtype isolates are defined as those without E484K or N501Y mutations. For comparisons based on lineage, B.1.526-E484K was compared with non-variant of interest (VOI) and non-variant of concern (VOC) lineages (i.e. B.1.526.1, B.1.526.2, B.1.1.7, P.1, P.2, and B.1.351 were excluded). Comparisons were made using the first genotyped sample per patient to exclude multiple measures.
T-tests (two-sided) were performed for continuous variables and chi-squared tests for categorical variables, unless otherwise indicated as below
Due to non-normal distribution, Kruskal-Wallis non-parametric test was used
Cycle threshold value as determined through our rapid qPCR-based screening assay on heat-inactivated nasopharyngeal swab samples