Uncategorized

Inclusivity_UK variant

 Inclusivity_UK variant (B.1.1.7./VUI202012/01) 

  •  The in silico analysis was performed to determine the reactivity of “KimForest SARS-CoV-2 Detection Kit v1” against variant SARS-CoV-2 isolates grouped in VUI202012/01 Variants/Subs. All SARS-CoV-2 genomes available from GISAID on 11/26/2020 were downloaded. The genome enrolled for in silico analysis should meet the criteria: 1. selection VUI202012/01; 2. Genome length >29,000 bp; 3. N proportion (not specific A, T, C, G) <5 % of genome; 4. Human source. A total of 334 isolates met the criteria were enrolled. The 334 viral genomes were aligned against RdRp primers and probe used in KimForest SARS-CoV-2 Detection Kit v1. The number of mismatches against primers and the probe in the deposited viral genomes were measured and listed in the summary table below. According to inclusivity study results, all isolates sequences showed less than or equal to 1 base mismatch within the primer/probe aligned region. For the SARS RdRp_R inclusivity study, SARS RdRp_R was designed with 26 nucleotides in length, and all 334 isolates sequences showed 1 mismatch against the SARS RdRp_R sequence. For the SARS RdRp_F and SARS RdRp_P inclusivity studies, SARS RdRp_F and SARS RdRp_P were designed with 22 and 25 nucleotides in length, respectively, and all 334 isolates sequences showed the 100% sequence identity to both SARS RdRp_F and SARS RdRp_P. Therefore, we speculated KimForest SARS-CoV-2 Detection Kit v1 might possibly detect these variant SARS-CoV-2 isolates. 
  •  Summary table, In silico analysis summary for inclusivity of primer/probe and SARS-CoV-2 isolates grouped in VUI202012/01 Variants/Subs. Perfect mismatch  1 base match  Total isolates 
    SARS RdRp_F  334  0  334 
    SARS RdRp_R  0  334  334 
    SARS RdRp_P  334  0  334 

 

Leave a Reply

Your email address will not be published. Required fields are marked *