Table 2.

Comparison of primer sets developed by WHO referral labs, against the primer set obtained by the proposed approach, listed as UtrechtU-ORF3a.

Primer	Sequence	Frequency (%)	Specific (Yes/No)
Charite-E-F	5′-ACA GGT ACG TTA ATA GTT AAT AGC GT-3′	99.90	No
Charite-E-R	5′-ATA TTG CAG CAG TAC GCA CAC A-3′	99.90	No
CHINA-CDC-ORF1ab-F	5′-CCC TGT GGG TTT TAC ACT TAA-3′	99.90	Yes
CHINA-CDC-ORF1ab-R	5′-ACG ATT GTG CAT CAG CTG A-3′	99.59	Yes
HKU-N-F	5′-TAA TCA GAC AAG GAA CTG ATT A-3′	99.56	No
HKU-N-R	5′-CGA AGG TGT GAC TTC CAT G-3′	99.58	No
US-CDC-N1-F	5′-GAC CCC AAA ATC AGC GAA AT-3′	99.71	Yes
US-CDC-N1-R	5′-TCT GGT TAC TGC CAG TTG AAT CTG-3′	99.57	Yes
US-CDC-N2-F	5′-TTA CAA ACA TTG GCC GCA AA-3′	99.43	No
US-CDC-N2-R	5′-GCG CGA CAT TCC GAA GAA-3′	99.74	Yes
UtrechtU-ORF3a-F	5′-TAG CAC TCT CCA AGG GTG TTC-3′	99.57	Yes
UtrechtU-ORF3a-R	5′-GCA AAG CCA AAG CCT CAT TA-3′	99.48	Yes
US-CDC-N3-F	5′-GGG AGC CTT GAA TAC ACC AAA A-3′	99.09	Yes
US-CDC-N3-R	5′-TGT AGC ACG ATT GCA GCA TTG-3′	99.72	Yes
CHINA-CDC-N-F	5′-GGG GAA CTT CTC CTG CTA GAA T-3′	68.52	Yes
CHINA-CDC-N-R	5′-CAG ACA TTT TGC TCT CAA GCT G-3′	99.20	Yes

The Frequency column indicates frequency of appearance of the sequence among samples of the GISAID dataset. The Specific (Yes/No) column shows whether the sequence appears to be unique to SARS-CoV-2 samples, or can also be found in other viruses, according to the evaluation on the NCBI-B and NGDC datasets.