Table 3 Summary of the most frequent mutations in the TRs of investigated PCR primer systems.

From: Identification of mutations in SARS-CoV-2 PCR primer regions

Primer

Mutation

Mutation consequence

Defining mutation in VOC

Ratio of mutated samples in the CoVEO database (%)

Ratio of mutated samples by WHO designation (*)

Sarkar-S-FM

SNP: C21618G

S: T19R

Delta

50.52

Delta (89.13%), other variant (9.15%)

Corman-RdRp-FH, Niu-RdRp-FH, Tombuloglu-RdRp-FM, Won-RdRp-1-FM

SNP: G15451A

Synonymous

–

50.03

Delta (87.79%), other variant (10.04%), Beta (< 1%), Omicron (< 1%), Alpha (< 1%), Gamma (< 1%)

Niu-N-FM

SNP: G28881T

N: R203M

Delta

44.83

Delta (79.16%), other variant (7.98%), Alpha (< 1%)

Niu-N-FH

“AAC”-triplet: G28881A, G28882A, G28883C

N: R203K, G204R

Alpha, Omicron

29.07

Omicron (90.62%), Gamma (90.19%), Alpha (84.93%), other variant (45.36%), Delta (< 1%)

Young-S-FH

Deletion: ATACATG21764A

S: H69_V70del

Alpha, Omicron

17.40

Omicron (64.04%), Alpha (58.33%), other variant (22.17%), Delta (< 1%)

Davi-S-1-PM, Davi-S-2-PM

SNP: C23271A

S: A570D

Alpha

16.52

Alpha (93.98%), other variant (2.99%), Delta (< 1%)

Niu-N-RM

SNP: C28977T

N: S235F

Alpha

12.88

Alpha (74.97%), other variant (1.19%), Gamma (< 1%), Delta (< 1%)

Sarkar-E-FH, Corman-E-FM, Mollaei-E-FM, Tombuloglu-E-FM, Won-E-1-FM, Won-E-2-FM

SNP: C26270T

E: T9I

Omicron

11.06

Omicron (77.52%), other variant (33.93%), Alpha (< 1%), Gamma (< 1%), Delta (< 1%), Beta (< 1%)

Lu-N-1-probeM

SNP: C28311T

N: P13L

Omicron

10.20

Omicron (58.86%), other variant (33.0%), Beta (< 1%), Gamma (< 1%), Delta (< 1%), Alpha (< 1%)

  1. For more details, regarding mutation position and estimated effect in the different primers, see Supplementary Table 1.
  2. Primer names are based on the nomenclature: [first author last name]-[target gene name]-[id, when multiple primer systems target the same gene]-[type of oligo: forward (F), reverse (R) or probe (P)]. “M” marks the primers where the variant was defined as a moderate-risk mutation; “H” marks the primers if the variant was defined as a high risk mutation. Mutation names are based on the nomenclature: [reference base][genomic position of the start of the variant][alternate non-reference base]. Asterisk: ratio of samples which contain the mutation in a given WHO designation. In the fourth column, those VOCs are listed in which the given mutation appears as a defining one. Lineages with no mutated samples are not listed.
  3. SNP single-nucleotide polymorphism.
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