Table 1.
Sequences of primers used for synthesis of PCR amplicons that include SARS-CoV-2 genome sequence variations of interesta.
| Amplicon no. | Genomic region within amplicon | Primer sequences (5ˈ- 3ˈ)b | Target Tag SNV/haplotype | Other sequence variations of interest within the amplicon |
|---|---|---|---|---|
| 1 | 13961–14601 | F: TATACGCCAACTTAGGTGAACG | 14408C>T/H1 | |
| R: TAGATTACCAGAAGCAGCGTG | ||||
| 2 | 21770–22446 | F: GTCTCTGGGACCAATGGTAC | 22227C>T/H1r | 21991-21993delTTA/B.1.1.7 |
| R: GGGTCAAGTGCACAGTCTAC | ||||
| 3 | 22855–23562 | F: CTGCGTTATAGCTTGGAATTCT | 23403A>G/H1 | 23012G>A/B.1.351; 23063A>T/B.1.1.7 & B.1.351; 23271C>A/B.1.1.7 |
| R: CCAATGGGTATGTCACACTCA | ||||
| 4 | 25318–25940 | F: CTGCTGCAAATTTGATGAAGAC | 25563G>T/H1b | |
| R: TCATGTTCAGAAATAGGACTTGT | ||||
| 5 | 28497–29161 | F: ACACCAATAGCAGTCCAGATG | 28881_28883GGG>AAC/H1a | 28688T>C/H5; 28932C>T/H1r; 28977C>T/B.1.1.7 |
| R: AGTTCCTTGTCTGATTAGTTCCT |
a
, The cDNAs pertaining to amplicons 1 and 3 were usually synthesized together in a single cDNA synthesis reaction, as were the cDNAs pertaining to amplicons 4 and 5.
b
Reverse (R) primers were used in all of the cDNA synthesis reactions.