Figure 4 | Scientific Reports

Figure 4

From: Development and validation of cost-effective SYBR Green-based RT-qPCR and its evaluation in a sample pooling strategy for detecting SARS-CoV-2 infection in the Indonesian setting

Figure 4

Sequence variants in primer binding regions for N158 primer forward (A) and reverse (B). A total of 998 SARS-CoV-2 genome sequences from infected individuals of Indonesia, including delta (n = 250), omicron and its subvariants BA.1, BA.2, BA.3, BA.4.1, BA.5, BF.5 and XBB.1 (n = 748) submitted from November 2021 until the end of May 2023 were downloaded from the GISAD database (https://www.gisaid.org/). Using Bioedit Sequence Alignment Editor, each primer was aligned to the genome sequences to calculate nucleotide diversity and investigate mismatches to the genome sequence sets. The position and frequency of each variant/mismatch on the primers was then plotted.

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