qPCR/PCR |
B.1.1.7 (Alpha) |
N501Y |
LOD: 4 RNA copies/reaction, Sensitivity and specificity: 100% (MC) |
[303] |
B.1.1.7 (Alpha), B.1.351 (Beta), |
N501Y, E484K |
LOD: 10 RNA copies/reaction |
[302] |
B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma) |
N501Y |
LOD:5000 RNA copies/mL, sensitivity and specificity = 100% |
[301] |
B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma) |
K417N, N501Y |
Sensitivity of PCR to detect VOC could be 10% better than whole genome sequencing |
[305] |
Almost all variants |
N501Y, E484K, K417N |
RT-PCR and melt curve analyses were able to detect 80% of alpha, 5% of beta, 2% of gamma and 13% of non-variants of SARS-CoV-2 from 989 samples |
[344] |
Almost all variants |
N501Y, D614G |
LOD: 100 RNA copies/mL, specificity unclear |
[304] |
Almost all variants |
N501Y, 69del, 70del, K417N, and E484K |
Sensitivity and specificity unclear |
[345] |
B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma) |
E484K |
LOD: 1–100 copies/μL |
[69] |
Sensitivity and specificity: cannot differentiate all VOC/VOI |
Nucleic acid sequencing |
B.1.1.7 (Alpha) |
N501Y |
LOD:18.5 RNA copies/reaction, sensitivity and specificity unclear |
[308] |
B.1.1.7 (Alpha) |
P681H, E484K |
Nucleic acid sequencing is able to differentiate B.1.1.7 (58%) and non-B1.1.7 infection (42%) |
[306] |
B.1.1.7 (Alpha), B.1.1.162. B.1.1.267, B.1.1 |
D614G, A222V, S982A, T716I, P681H, A570D, E583D |
Nucleic acid sequencing was able to detect more than 60% of the SARS-CoV-2 variants from different samples collected from different infection waves. |
[307] |
B.1.351 (Beta) |
K417N, E484K, N501Y |
Number of accumulated amino acid changes in whole genome = 341 |
[338] |
PCR + Nucleic acid sequencing |
B.1.1.7 (Alpha) |
N501Y, S477N and D614G |
LOD: Only samples with Cq value < 25 for N gene could be detected using WGS. Specificity: Unclear |
[309] |
Almost all variants |
69del, 70del, Y144del, N501Y and A570D |
Compared to WGS, RT-PCR and sanger sequencing require shorter time and lower cost. LOD unclear |
[310] |
SNP genotyping |
Almost all variants |
Unreported |
>62% to be able to distinguish two variants of different genotypes |
[311] |
RT-LAMP |
P.1 (Gamma), P.2 (Zeta) |
N501Y, E484K/Q, K417N/T |
Sensitivity: 97%, Specificity: 100% (based on N/E targets) |
[312] |
B.1.1.7 (Alpha) |
69del, 70del |
LOD: 39–10,000 RNA copies/reaction |
[313] |
CRISRP/Cas-based technique |
B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma) |
N501Y |
LOD, sensitivity and specificity unclear |
[346] |
Almost all variants have D614G |
D614G |
LOD: 10 RNA copies/reaction |
[314] |
Other variants |
E174R/S542R/K548R, S254F |
LOD: 50–1000 RNA copies/reaction, specificity: 100% |
[315] |
Almost all variants have D614G |
D614G |
LOD: 82 RNA copies/reaction, % specificity unclear |
[155] |
Antigen test |
B.1.1.7 (Alpha), B.1.351 (Beta), |
Unclear |
LOD: 1.7 × 105 – 6.6 × 107 RNA copies/mL |
[316] |
Sensitivity and specificity: Unclear |
Antigen and antibody test |
B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma) |
Unclear |
Detection rate of antigen/antibody tests to detect these three variants were reported to be >90% |
[317] |