Skip to main content
. 2021 Jul 24;225:153565. doi: 10.1016/j.prp.2021.153565

Table 19.

Detection of various SARS-CoV-2 variants using different methods.

Methods Types of detectable variants Examples of detectable mutations Key findings References
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]