TABLE 1.
Patient characteristics and aggregate genotyping RT-qPCR screening results during the study period
| Characteristic(s) | Valuea in: |
||
|---|---|---|---|
| All SARS-CoV-2 infection group | RT-qPCR population | WGS validation subset | |
| Patients | 11,636 | 4,049 | 229 |
| Age at first positive NAAT (yr [range]) | 36 [23–52] | 37 [23–53] | 37 [23–52] |
| Female | 6,009 (51.64) | 2,065 (51.00) | 128 (55.90) |
| Initial diagnostic specimen | |||
| Month of diagnosis | |||
| December 2020 | 6,074 (52.20) | 344 (8.50) | 18 (7.86) |
| January 2021 | 4,381 (37.65) | 3,050 (75.33) | 170 (74.24) |
| February 2021 | 1,119 (9.62) | 640 (15.80) | 37 (16.16) |
| March 2021 | 62 (0.53) | 15 (0.37) | 4 (1.75) |
| Specimen collection site | |||
| Outpatient COVID-19 screening site | 6,187 (53.18) | 2,393 (59.10) | 138 (60.26) |
| Emergency department | 2,633 (22.62) | 704 (17.39) | 34 (14.85) |
| Outpatient laboratory | 1,190 (10.23) | 469 (11.58) | 24 (10.48) |
| Occupational health | 628 (5.40) | 123 (3.04) | 6 (2.62) |
| Outpatient clinic | 564 (4.85) | 210 (5.19) | 20 (8.73) |
| Urgent care | 220 (1.89) | 75 (1.85) | 6 (2.62) |
| Inpatient floor | 154 (1.32) | 55 (1.36) | 1 (0.43) |
| Perioperative/periprocedural | 28 (0.24) | 11 (0.27) | 0 (0.00) |
| Intensive care unit | 20 (0.17) | 4 (0.10) | 0 (0.00) |
| Infusion center | 10 (0.09) | 3 (0.07) | 0 (0.00) |
| Home health care | 2 (0.02) | 2 (0.05) | 0 (0.00) |
| Specimen source | |||
| Nasopharyngeal swab | 6,607 (56.78) | 1,965 (48.51) | 115 (50.22) |
| Mid-turbinate nasal swab | 4,893 (42.05) | 2,077 (51.30) | 111 (48.48) |
| Other | 136 (1.17) | 7 (0.17) | 3 (1.30) |
| NAAT platform | |||
| PerkinElmer-based RT-qPCR | 7,004 (60.19) | 2,798 (69.10) | 157 (68.56) |
| Lab-developed RT-qPCR | 2,418 (20.78) | 610 (15.07) | 44 (19.21) |
| Hologic Panther | 1,219 (10.48) | 353 (8.72) | 25 (10.92) |
| Cepheid GeneXpert | 573 (4.92) | 147 (3.63) | 1 (0.44) |
| Roche Liat | 320 (2.75) | 97 (2.40) | 0 (0.00) |
| Genmark Eplex | 102 (0.88) | 44 (1.09) | 2 (0.87) |
| RT-qPCR genotype | |||
| L452, E484, N501 | — | 2,308 (57.00) | 120 (52.40) |
| L452R, E484, N501 | — | 1,567 (38.70) | 70 (30.57) |
| L452, E484K, N501 | — | 22 (0.54) | 14 (6.11) |
| L452, E484, N501Y | — | 34 (0.84) | 22 (9.61) |
| L452, E484K, N501Y | — | 3 (0.07) | 3 (1.30) |
| Unable to genotypeb | — | 115 (2.84) | 0 (0.00) |
a
Values are numbers (percentages) unless otherwise indicated. —, not applicable.
b
Low viral load, amplification failure, or reaction setup failure despite repeated testing.