Table 4. Comparison of 5-SSG primers target mutations sequence of Sanger sequencing and NGS.
| Grades of concern | Lineage | Source | Sequence analysis method | Final Determination | |
|---|---|---|---|---|---|
| NGS | Sanger sequencing | ||||
| VOC | B.1.1.7 | Twistbio-710528 | ΔH69/V70, ΔY144, N501Y, A570D, D614G, P681H, T716I | ΔH69/V70, ΔY144, N501Y, A570D, D614G, P681H, T716I | Match |
| Twistbio-601443 | ΔH69/V70, ΔY144, N501Y, A570D, D614G, P681H, T716I | ΔH69/V70, ΔY144, N501Y, A570D, D614G, P681H, T716I | Match | ||
| NCCP-43381 | ΔH69/V70, ΔY144, N501Y, A570D, D614G, P681H, R682Q, T716I | ΔH69/V70, ΔY144, N501Y, A570D, D614G, P681H, R682Q, T716I | Match | ||
| B.1.351 | Twistbio-678597 | D80A, D215G, ΔLAL242-244, K417N, E484K, N501Y, D614G, A701V | D80A, D215G, ΔLAL242-244, K417N, E484K, N501Y, D614G, A701V | Match | |
| NCCP-43382 | L54F, D80A, D215G, ΔLAL242-244, K417N, E484K, N501Y, D614G, A701V | L54F, D80A, D215G, ΔLAL242-244, K417N, E484K, N501Y, D614G, A701V | Match | ||
| P.1 | Twistbio-79683 | D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y | D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y | Match | |
| B.1.617.2 | NCCP-43390 | G142D, ΔE156/F157, R158G, L452R, T478K, Q613H, D614G, P681R, R682W | G142D, ΔE156/F157, R158G, L452R, T478K, Q613H, D614G, P681R, R682W | Match | |
| VOI | B.1.427 | NCCP-43384 | W152C, L452R, D614G | W152C, L452R, D614G | Match |
| B.1.429 | NCCP-43385 | W152C, L452R, D614G | W152C, L452R, D614G | Match | |
| B.1.525 | NCCP-43386 | Q52R, A67V, ΔH69/V70, ΔY144, E484K, D614G, Q677H | Q52R, A67V, ΔH69/V70, ΔY144, E484K, D614G, Q677H | Match | |
| B.1.526 | NCCP-43387 | T95I, D253G, E484K, D614G, H655Y, A701V | T95I, D253G, E484K, D614G, H655Y, A701V | Match | |
| B.1.617.1 | NCCP-43389 | G142D, E154K, L452R, E484Q, D614G, P681R, R682Q | G142D, E154K, L452R, E484Q, D614G, P681R, R682Q | Match | |
| Not included | P.2 | NCCP-43383 | E484K, D614G | E484K, D614G | Match |
| B | NCCP-43330 | - | - | Match | |
| A | NCCP-43331 | H655Y | H655Y | Match | |
| B | NCCP-43342 | - | - | Match | |
| B.1.1- | NCCP-43343 | D614G, R682Q | D614G, R682Q | Match | |
| B.1- | NCCP-43344 | D215H, D614G, R682Q | D215H, D614G, R682Q | Match | |
| B.1.497 | NCCP-43345 | D614G, ΔQTQTN675-679, R682L | D614G, ΔQTQTN675-679, R682L | Match | |
| A | Zeptometrix -0810587CFHI |
D215/L216insKLRS, ΔQTQTN675-679 | D215/L216insKLRS, ΔQTQTN675-679 | Match | |
| B | Zeptometrix -0810589CFHI |
N74K, S247R, ΔNSPRRARSVA679-688 | N74K, S247R, ΔNSPRRARSVA679-688 | Match | |
| A | Zeptometrix -0810590CFHI |
S247R, V367F, R682Q, | S247R, V367F, R682Q | Match | |
Abbreviations: VOC, Variant of concern; VOI, variant of interest; Δ, deletion. Low-coverage NGS data are marked in underline.