Table 3 Comparison of SARS-CoV-2 variant identification using Next Generation Sequencing (NGS) and MassARRY PMA-ABDO and PMA-Omicron (n = 358).
SARS-CoV-2 PCR Ct (N gene) | SARS-CoV-2 variant NGS examination (n) | PMA panel assay | SARS-CoV-2 variant PMA result (detected/tested) | |
|---|---|---|---|---|
MassARRAY call rate > 43.59% | MassARRAY call rate < 43.59% | |||
Group 1: SARS-CoV-2 positive sample with PCR Ct < 26 (n = 256) | ||||
< 26 | Alpha (58) | ABDO | Alpha (58/58) | 0/58 |
< 26 | Beta (3) | ABDO | Beta (3/3) | 0/3 |
< 26 | Delta (112) | ABDO | Delta (112/112) | 0/112 |
< 26 | Gamma (1) | ABDO | Gamma (1/1) | 0/1 |
< 26 | Non-VOC* (23) | ABDO | Non-VOC (23/23) | 0/23 |
< 26 | Omicron (BA.1) (20) | Omicron | B.1.1.529 or BA.x (20/20) | 0/20 |
< 26 | Omicron (BA.1.1) (16) | Omicron | B.1.1 (16/16) | 0/16 |
< 26 | Omicron BA.2 (23) | Omicron | BA.2 (23/23) | 0/23 |
Group 2: SARS-CoV-2 positive sample with PCR Ct > 26 and NGS failed for variant characterization (n = 28) | ||||
28.33–35.54 | Fail (14) | ABDO | Alpha (11/14) | Possible Alpha (3/14) |
29.33–39.94 | Fail (9) | ABDO | Delta (9/9) | 0/9 |
26.0–37.92 | Fail (5) | Omicron | Omicron (B.1.1.529 or BA.x) (5/5) | 0/5 |
Group 3: SARS-CoV-2 positive sample with PCR Ct > 30 without NGS result (n = 74) | ||||
30.06–38.83 | NA | ABDO | Alpha (41/41) | 0/41 |
30–35.45 | NA | ABDO | Delta (14/14) | 0/14 |
30–39.1 | NA | Omicron | Omicron (B.1.1.529 or BA.x) (19/19) | 0/19 |
