Fig 1.
How the SARS-CoV-2 genotyping panel can be used to identify circulating SARS-CoV-2 variants.
Table 1.
Laboratory samples used to validate the SARS-CoV-2 test genotyping panel.
Fig 2.
a) The RNA sample, which here contains two SNP variants, is reverse transcribed to produce single stranded DNA. b) The target region is then amplified using two, allele specific primers which differ in their 3’ terminal base and 5’ tail, and a common reverse primer. As PCR proceeds, the tail sequences of allele-specific forward primers become incorporated in the amplified fragments and their sequence complements are generated. c) Reporting cassettes, initially quenched, bind to the appropriate tail sequence complement, become unquenched and produce a light signal (HEX (red), FAM (blue)). d) Fluorescence intensity is measured and plotted to determine allele calls. A mixed signal (green) is seen as equal signal from both fluorochromes. Samples at the origin are the no-template controls (black) and unamplified samples (pink).
Table 2.
Alternative SNPs and their effect on protein coding.
Table 3.
Comparison of genotyping and sequencing data obtained for the test set.
Fig 3.
Genotyping calls for all samples.
SNPs with a single allele call per sample are marked in dark blue (major allele) or orange (minor allele). Mixed calls are shown in gold and missing data in light blue. Twelve out of 19 markers were polymorphic in our small test panel of PHE samples and cell lines (eleven out of 19 markers were polymorphic in PHE samples) and eight samples had mixed calls for one or more markers.