Table 3.
SARS-CoV-2 genomic sequence variants at locations targeted by three early lab developed tests with substantial mismatches. Mismatched nucleotides are bolded and underlined. For convenience, genome locations are expressed as DNA sequences from the strand containing the assay oligonucleotide (top strand for forward primers and probes and bottom strand for reverse primers). Only variants present in at least 1% of all genomes in the dataset are shown (table with all variants available as Supplementary Table S1).
| Assay | Oligonucleotide | Variant genome sequence at target location | Mismatches | Frequency among all genomes |
|---|---|---|---|---|
| Charité group - RdRP | Forward primer | 5′ GTGAAATGGTCATGTGTGGCGG 3’ | 0 | 99.7 % |
| Probe | 5′ CAGGTGGAACCTCATCAGGAGATGC 3’ | 0 | 99.9% | |
| Reverse primer | 5′ CAAATGTTAAAAACACTATTAGCATA 3’ | 1 | 100.0 % | |
| Japan NIID - N | Forward primer | 5′ AAATTTTGGGGACCAGGAAC 3’ | 0 | 99.7 % |
| Probe | 5′ ATGTCGCGCATTGGCATGGA 3’ | 0 | 99.9% | |
| Reverse primer | 5′ TGGCACCTGTGTAGGTCAAC 3’ | 1 | 99.8% | |
| China CDC - N | Forward primer | 5′ GGGGAACTTCTCCTGCTAGAAT 3’ | 0 | 80.1 % |
| 5′ AACGAACTTCTCCTGCTAGAAT 3’ | 3 | 18.8 % | ||
| Probe | 5′ TTGCTGCTGCTTGACAGATT 3’ | 0 | 100.0 % | |
| Reverse primer | 5′ CAGACATTTTGCTCTCAAGCTG 3’ | 0 | 99.8% |