2025 SARS-CoV-2 Sequences with Diagnostic Primer/Probe Mismatch Profiles (Q1 - Q3)

A collection of 46,253 SARS-CoV-2 genomes from early-to-mid 2025 (Q1-Q3), annotated with detailed mismatch profiles against 11 globally used diagnostic primer and probe regions. Each sequence includes a QC report identifying nucleotide variations within primer binding and probe hybridization sites, based on alignment to Wuhan-Hu-1 (NC_045512.2). Data supports ongoing evaluation of molecular diagnostic assay performance against evolving SARS-CoV-2 variants.Sequences with ≥1 PROBE mismatch: 44,496 (96.2%) Top 10 Most Impacted Assays: N_gene_China: 183,018 sequences (395.7%) ORF1ab_China_Set1: 85,066 sequences (183.9%) N1_USA: 69,354 sequences (149.9%) E_gene_Germany: 44,296 sequences (95.8%) RdRp_Germany: 4,569 sequences (9.9%) N2_USA: 3,845 sequences (8.3%) N_gene_HongKong: 3,512 sequences (7.6%) N3_USA: 1,996 sequences (4.3%) N_gene_Japan: 1,098 sequences (2.4%) N_gene_Thailand: 836 sequences (1.8%) Top 10 Most Mutated Primer/Probe Regions: N_gene_China_forward (forward): 142,820 mutations N1_USA_probe (probe): 44,535 mutations E_gene_Germany_forward (forward): 44,240 mutations ORF1ab_China_Set1_forward (forward): 44,088 mutations ORF1ab_China_Set1_probe (probe): 40,772 mutations N_gene_China_reverse (reverse): 40,078 mutations N1_USA_forward (forward): 24,439 mutations RdRp_Germany_forward (forward): 4,369 mutations N2_USA_forward (forward): 3,240 mutations N_gene_HongKong_forward (forward): 3,092 mutations Top 15 Most Frequently Mutated Genomic Positions: Position 28881: 45,651 mutations Position 28882: 44,386 mutations Position 28883: 44,385 mutations Position 26270: 44,083 mutations Position 28311: 44,005 mutations Position 15714: 43,868 mutations Position 28958: 39,645 mutations Position 15756: 39,407 mutations Position 28297: 16,214 mutations Position 28884: 8,157 mutations Position 28291: 7,937 mutations Position 29164: 5,976 mutations Position 15451: 4,321 mutations Position 15762: 775 mutations Position 28681: 516 mutations Distribution of # Assays Impacted per Sequence: 0 assays (fully intact): 133 (0.3%) 1 assays: 398 (0.9%) 2 assays: 1,137 (2.5%) 3 assays: 1,326 (2.9%) 4 assays: 35,407 (76.6%) 5 assays: 4,493 (9.7%) 6 assays: 497 (1.1%) 7 assays: 2,630 (5.7%) 8 assays: 225 (0.5%) 9 assays: 7 ~(0.0%)Processed by: [e-mail]