2024 SARS-CoV-2 Sequences with Diagnostic Primer/Probe Mismatch Profiles

A collection of 142,981 SARS-CoV-2 genomes from 2024, 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 derived from high-throughput analysis of aligned FASTA sequences and intended for use in diagnostic assay validation and variant surveillance.Sequences with ≥1 PROBE mismatch: 140,948 (98.6%) Top 10 Most Impacted Assays (by # of sequences): N_gene_China: 568,780 sequences (397.8%) ORF1ab_China_Set1: 275,297 sequences (192.5%) N1_USA: 158,949 sequences (111.2%) E_gene_Germany: 144,591 sequences (101.1%) N3_USA: 10,445 sequences (7.3%) RdRp_Germany: 6,788 sequences (4.7%) N2_USA: 2,217 sequences (1.6%) N_gene_Japan: 2,204 sequences (1.5%) N_gene_Thailand: 1,949 sequences (1.4%) N_gene_HongKong: 1,936 sequences (1.4%) Top 10 Most Mutated Primer/Probe Regions: N_gene_China_forward (forward): 434,349 mutations E_gene_Germany_forward (forward): 144,387 mutations N1_USA_probe (probe): 141,012 mutations ORF1ab_China_Set1_forward (forward): 140,561 mutations ORF1ab_China_Set1_probe (probe): 134,458 mutations N_gene_China_reverse (reverse): 133,763 mutations N1_USA_forward (forward): 17,063 mutations N3_USA_probe (probe): 8,144 mutations RdRp_Germany_forward (forward): 6,352 mutations N3_USA_forward (forward): 1,281 mutations Top 15 Most Frequently Mutated Genomic Positions: Position 28881: 141,598 mutations Position 28883: 140,394 mutations Position 28882: 140,352 mutations Position 15714: 140,080 mutations Position 28311: 139,897 mutations Position 26270: 139,666 mutations Position 15756: 133,601 mutations Position 28958: 133,143 mutations Position 28884: 11,377 mutations Position 28291: 11,223 mutations Position 28714: 6,368 mutations Position 15451: 6,139 mutations Position 28297: 5,261 mutations Position 26275: 4,593 mutations Position 28344: 702 mutations Distribution of # Assays Impacted per Sequence: 0 assays (fully intact): 155 (0.1%) 1 assays: 523 (0.4%) 2 assays: 1,564 (1.1%) 3 assays: 2,477 (1.7%) 4 assays: 116,072 (81.2%) 5 assays: 20,219 (14.1%) 6 assays: 1,796 (1.3%) 7 assays: 171 (0.1%) 8 assays: 4 (0.0%) Data Processed by: [e-mail]