{"data_server":"https://primer-monitor.neb.com/igvstatic","organism_slug":"sars-cov-2","organism_name":"SARS-CoV-2","reference_accession":"NC_045512.2","primer_set_display_name":"NEBNext SARS-CoV-2 Primers","primer_set_name":"NEBNext_SARS-CoV-2_Primers","initial_lineage":"SW.2","lineage_names":{"TA.1":"TA.1*","RE.1.1":"RE.1.1*","RV.1.1":"RV.1.1*","RE.2":"RE.2*","PJ.2.1":"PJ.2.1*","ST":"ST*","PG.3.2":"PG.3.2*","RV":"RV*","B":"B*","TK.1":"TK.1*","SW.2":"SW.2*","SW.2.1":"SW.2.1*","RE.1":"RE.1*","RW":"RW*","XFZ":"XFZ*","RE.2.1":"RE.2.1*","BA.2.86":"BA.2.86*","SW":"SW*","B.60":"B.60*","SB":"SB*","SV":"SV*","PG":"PG*","ST.1":"ST.1*","RF":"RF*","TA":"TA*","RW.1":"RW.1*","A":"A*","RE":"RE*","SV.1":"SV.1*","RW.1.1":"RW.1.1*","RV.1.1.1":"RV.1.1.1*","TK":"TK*","PJ":"PJ*","RV.1":"RV.1*","PJ.2":"PJ.2*","PG.3":"PG.3*","all":"All"},"variant_overlaps_path":"/organisms/sars-cov-2/lineage_variants/variant_overlaps.json"}
Variants seen recently in the selected lineage are shown in gray below the genome. Primers that overlap enough sufficiently-frequent variants to be potentially impacted are shown in orange, others in blue. See Primer Status for how impact is scored.
| Name | Locus | Category | Sequence |
|---|---|---|---|
| varskip-0317-1_01_LEFT_ALT3 | Forward | ATCTCTTGTAGATCTGTTCTCTAAACG | |
| varskip-0317-1_01_RIGHT | CACCAAGTGTCTCACCACTACG | ||
| varskip-0317-1_02_LEFT | GGCTTAGTAGAAGTTGAAAAAGGCG | ||
| varskip-0317-1_02_RIGHT | AACGTTCCGTGTACCAAGCAAT | ||
| varskip-0317-1_03_LEFT | CCTGATGGCTACCCTCTTGAGT | ||
| varskip-0317-1_03_RIGHT | ATTCGGCAAGACTATGCTCAGG | ||
| varskip-0317-1_04_LEFT | AAGCCACTTGCGAATTTTGTGG | ||
| varskip-0317-1_04_RIGHT | TCTGTTCACCAATATTCCAGGCA | ||
| varskip-0317-1_05_LEFT | GGCATCTTTTTCTGCTTCCACA | ||
| varskip-0317-1_05_RIGHT | CCACCGACAATTTCACAAGCAC | ||
| varskip-0317-1_05_RIGHT_ALT2 | GACAATTTCACAAGCACAGGTTGAG | ||
| varskip-0317-1_06_LEFT | CTACATTACAGGTGGTGTTGTTCAG | ||
| varskip-0317-1_06_RIGHT | ATTTCGAGCAACATAAGCCCGT | ||
| varskip-0317-1_07_LEFT | TCTTCTTAGAGGGAGAAACACTTCC | ||
| varskip-0317-1_07_LEFT_ALT2 | CCTCTAAAAGCCCCAAAAGAAATTATC | ||
| varskip-0317-1_07_RIGHT | ACCTTCTTCTTCATCCTCATCTGG | ||
| varskip-0317-1_08_LEFT | TCTGAATTACTTACACCACTGGGC | ||
| varskip-0317-1_08_RIGHT | TTTAAGGCTCCTGCAACACCTC | ||
| varskip-0317-1_09_LEFT | AGACTATTGAAGTGAATAGTTTTAGTGGT | ||
| varskip-0317-1_09_RIGHT | TCAGTTATAAATGGCTTAACTTCCTCTT | ||
| varskip-0317-1_09_RIGHT_ALT2 | GTTTACTTTCAGTTATAAATGGCTTAACTTC | ||
| varskip-0317-1_10_LEFT | AGTTTGTGTAGATACTGTTCGCACA | ||
| varskip-0317-1_10_RIGHT | AGGCACTTTTACACTTTTTAAGCACT | ||
| varskip-0317-1_11_LEFT | CTGCTGTGGTTATACCTACTAAAAAG | ||
| varskip-0317-1_11_LEFT_ALT2 | GTGGCACTACTGAAATGCTAGC | ||
| varskip-0317-1_11_RIGHT | GAAGAAGTAAGATAACCATTATACGCTGT | ||
| varskip-0317-1_12_LEFT | ACTCTTGTTACAATGCCACTTGG | ||
| varskip-0317-1_12_RIGHT | AGTACTCAAAAGCCTCAACACGT | ||
| varskip-0317-1_13_LEFT | CGCAAGTTGTGGACATGTCAAT | ||
| varskip-0317-1_13_RIGHT | CCCATGTACATAACAGCTTCTACAC | ||
| varskip-0317-1_13_RIGHT_ALT2 | TTCATAAGAAAGTGTGCCCATGTAC | ||
| varskip-0317-1_14_LEFT | ACCTGCTCTACAAGATGCTTATTACA | ||
| varskip-0317-1_14_RIGHT | GTACAAGATCAATTGGTTGCTCTG | ||
| varskip-0317-1_15_LEFT | ACTTTGTATTGCATAGACGGTGC | ||
| varskip-0317-1_15_RIGHT | GCGTCCTCTGACTTCAGTACAT | ||
| varskip-0317-1_15_RIGHT_ALT1 | GCTCCAAAGACAACGTATACACC | ||
| varskip-0317-1_16_LEFT | TTGTTACATAAACCTATTGTTTGGCATG | ||
| varskip-0317-1_16_RIGHT | AAGGCATATAATTAGTACAAACACGGT | ||
| varskip-0317-1_17_LEFT | TGTAGACAATTCTAGTCTTACTATTAAGAAACC | ||
| varskip-0317-1_17_RIGHT | CTAAACCACTAAGACAAACACTACAAG | ||
| varskip-0317-1_18_LEFT | TCAACCGCTGCTTTAGGTGTTT | ||
| varskip-0317-1_18_RIGHT | AGACATAAAAGGACCTTCTAACACCAT | ||
| varskip-0317-1_19_LEFT | TGGTTAGAATGTACATCTTCTTTGCA | ||
| varskip-0317-1_19_RIGHT | CCAACATCAGACACTAATGCCTG | ||
| varskip-0317-1_20_LEFT | TAATAACACTAAAGGTTCATTGCCTATTAATG | ||
| varskip-0317-1_20_RIGHT | TGCGCATTAATATGACGCGCAC | ||
| varskip-0317-1_21_LEFT | TCTGACATAGAAGTTACTGGCGAT | ||
| varskip-0317-1_21_RIGHT | TTGTTATGACTGCAGCAATCAATGG | ||
| varskip-0317-1_22_LEFT | AGGATACAAGGCTATTGATGGTGG | ||
| varskip-0317-1_22_RIGHT | TCTGATCTTTCACAAGTGCCGT | ||
| varskip-0317-1_23_LEFT | TGAAAGTTTACGCCCTGACACA | ||
| varskip-0317-1_23_RIGHT | AGGTGTGAACATAACCATCCACT | ||
| varskip-0317-1_24_LEFT | GGTGAATACAGTCATGTAGTTGCC | ||
| varskip-0317-1_24_LEFT_ALT2 | GCCTTTAATACTTTACTATTCCTTATGTC | ||
| varskip-0317-1_24_RIGHT | AACCACTCTGCAAAACAGCTGA | ||
| varskip-0317-1_25_LEFT | TGCGTAGTGATGTGCTATTACCT | ||
| varskip-0317-1_25_RIGHT | GATGGTGAACCATTGTAACAAGCTAA | ||
| varskip-0317-1_26_LEFT | TGTTCAACTCAGGGTTATTGGACA | ||
| varskip-0317-1_26_RIGHT | AAACGGCAATTCCAGTTTGAGC | ||
| varskip-0317-1_27_LEFT | GGAGACAGGTGGTTTCTCAATCG | ||
| varskip-0317-1_27_RIGHT | TCCAACCATGTCATAATACGCATCA | ||
| varskip-0317-1_28_LEFT | GCCTTTTTACCTTTTGCTATGGGT | ||
| varskip-0317-1_28_RIGHT | CGGTTGAGTAAACAAAAGAGGCC | ||
| varskip-0317-1_28_RIGHT_ALT2 | AGGCCAAAGTAACAAGTACAAAAATAGC | ||
| varskip-0317-1_29_LEFT | GATGGTGCTAGGAGAGTGTGGA | ||
| varskip-0317-1_29_RIGHT | TGGACACATTGAGCCCACAATT | ||
| varskip-0317-1_30_LEFT | AAAGTAGCCACTGTACAGTCTAAAATG | ||
| varskip-0317-1_30_RIGHT | GCATAGCACTAGTAACTTTTGCCC | ||
| varskip-0317-1_31_LEFT | GTTGAAGAAGTCTTTGAATGTGGCT | ||
| varskip-0317-1_31_RIGHT | GCTAACGCATTGTCATCAGTGC | ||
| varskip-0317-1_32_LEFT | CATGGCCTCTTATTGTAACAGCTT | ||
| varskip-0317-1_32_RIGHT | ATTGCCTGACCAGTACCAGTGT | ||
| varskip-0317-1_32_RIGHT_ALT2 | CTGTTATTGCCTGACCAGTACC | ||
| varskip-0317-1_33_LEFT | CAACAGAAGTGCCTGCCAATTCAA | ||
| varskip-0317-1_33_RIGHT | CGTCCTTTTCTTGGAAGCGACA | ||
| varskip-0317-1_34_LEFT | GTAAGTGCAGCCCGTCTTACAC | ||
| varskip-0317-1_34_RIGHT | TCGCATGGCATCACAGAATTGT | ||
| varskip-0317-1_34_RIGHT_ALT2 | ATCACAGAATTGTACTGTTTTTAACAAAGC | ||
| varskip-0317-1_35_LEFT | ACTTGTCACATACAATTGTTGTGATGA | ||
| varskip-0317-1_35_LEFT_ALT2 | GATGATTATTTCAATAAAAAGGACTGGTATG | ||
| varskip-0317-1_35_RIGHT | ACAAATATTTTTCTCACTAGTGGTCCA | ||
| varskip-0317-1_36_LEFT | ACCGTTATTTTAAATATTGGGATCAGACA | ||
| varskip-0317-1_36_RIGHT | ACAAATAGTAGTTGTCTGATATCACACAT | ||
| varskip-0317-1_37_LEFT | TGTTGCTTTTCAAACTGTCAAACC | ||
| varskip-0317-1_37_RIGHT | TGCTTGTTCCAATTACTACAGTAGCT | ||
| varskip-0317-1_38_LEFT | TGAATCTTAAGTATGCCATTAGTGCAA | ||
| varskip-0317-1_38_RIGHT | AAAGTCTGTGTTGTAAATTGCGGA | ||
| varskip-0317-1_39_LEFT | GAGTGAAATGGTCATGTGTGGC | ||
| varskip-0317-1_39_RIGHT | AGCTAAAGACACGAACCGTTCA | ||
| varskip-0317-1_40_LEFT | GACCTCATGAATTTTGCTCTCAACA | ||
| varskip-0317-1_40_RIGHT | GCTCATACCTCCTAAGTAAAGTTGAGT | ||
| varskip-0317-1_41_LEFT | AAGATGTGGTGCTTGCATACGT | ||
| varskip-0317-1_41_RIGHT | ACAACAGCATCACCATAGTCACC | ||
| varskip-0317-1_42_LEFT | GCTACTGTACGTGAAGTGCTGT | ||
| varskip-0317-1_42_RIGHT | CAAAACAATCTACACGAGCACG | ||
| varskip-0317-1_43_LEFT | GCAAAAGTATTCTACACTCCAGGGA | ||
| varskip-0317-1_43_RIGHT | TTGAGCTGATTTGTCTTTATGTGCT | ||
| varskip-0317-1_44_LEFT | AGGGCACACTAGAACCAGAATATT | ||
| varskip-0317-1_44_RIGHT | AGTCCTGTTACATTTTCAGCTTGTAA | ||
| varskip-0317-1_45_LEFT | ACAGCTCACTCTTGTAATGTAAACAG | ||
| varskip-0317-1_45_RIGHT | GCGGTGGTTTAGCACTAACTCT | ||
| varskip-0317-1_45_RIGHT_ALT2 | ATTGATCTCCAGGCGGTGGTTT | ||
| varskip-0317-1_46_LEFT | CGAGGGGTGTCATGCTACTAGA | ||
| varskip-0317-1_46_RIGHT | ACACCTAGTCATGATTGCATCACA | ||
| varskip-0317-1_47_LEFT | CCTGTTGGCATCATTCTATTGGATT | ||
| varskip-0317-1_47_RIGHT | GCAAGTTAAGGTTAGATAGCACTCTA | ||
| varskip-0317-1_48_LEFT | CAGCCTTGTAGTGACAAAGCTTATAAA | ||
| varskip-0317-1_48_RIGHT | TTATTTACAACATTAAAAGCCACATTTTCTAA | ||
| varskip-0317-1_49_LEFT | TGTAGACATCATGCTAATGAGTACAGA | ||
| varskip-0317-1_49_RIGHT | AACACTACCTTCTGTAATAAGAACACC | ||
| varskip-0317-1_49_RIGHT_ALT1 | CATTACGGGCATTTCTAAATAAGTCTAC | ||
| varskip-0317-1_49_RIGHT_ALT2 | GTAATAAGAACACCATTACGGGCAT | ||
| varskip-0317-1_50_LEFT | AAAGAGATGCTCCAGCACATATATCT | ||
| varskip-0317-1_50_RIGHT | AGATGAACCTGTTTGCGCATCT | ||
| varskip-0317-1_51_LEFT | AGTCATAGTCAGTTAGGTGGTTTACA | ||
| varskip-0317-1_51_RIGHT | AAAACAGCTGTACCTGGTGCAA | ||
| varskip-0317-1_52_LEFT | CCTAAAGGCATAATGATGAATGTCGC | ||
| varskip-0317-1_52_RIGHT | TTTGCATGCATGACATAACCATCT | ||
| varskip-0317-1_53_LEFT | TCTTTATAAGCTCATGGGACACTTC | ||
| varskip-0317-1_53_RIGHT | CAAGTAACATTGGAAAAGAAAGGTAAGAA | ||
| varskip-0317-1_53_RIGHT_ALT2 | TGAGGATCTGAAAACTTTGTCAGG | ||
| varskip-0317-1_54_LEFT | GTTCTTGTTAACAACTAAACGAACAATGT | ||
| varskip-0317-1_54_RIGHT | CCCTGTTTTCCTTCAAGGTCCA | ||
| varskip-0317-1_54_RIGHT_ALT2 | CTTCAAGGTCCATAAGAAAAGGCT | ||
| varskip-0317-1_55_LEFT | ACGCTACTAATGTTGTTATTAAAGTCTGT | ||
| varskip-0317-1_55_LEFT_ALT1 | CCTACTTATTGTTAATAACGCTACTAATGTT | ||
| varskip-0317-1_55_RIGHT | AGAAGTTTGATAGATTCCTTTTTCTACAGT | ||
| varskip-0317-1_56_LEFT | TGCAGCTTATTATGTGGGTTATCTTC | ||
| varskip-0317-1_56_LEFT_ALT1 | TTATTATGTGGGTTATCTTCAACCTAGG | ||
| varskip-0317-1_56_RIGHT | TAGAATTCCAAGCTATAACGCAGC | ||
| varskip-0317-1_56_RIGHT_ALT2 | CAGCCTGTAAAATCATCTGGTAATTTAT | ||
| varskip-0317-1_57_LEFT | TGCAGATTCATTTGTAATTAGAGGTGA | ||
| varskip-0317-1_57_LEFT_ALT2 | ATGTCTATGCAGATTCATTTGTAATTAGAGG | ||
| varskip-0317-1_57_LEFT_ALT6 | CTCTGCTTTACTAATGTCTATGCAGA | ||
| varskip-0317-1_57_RIGHT | TCAAGTGTCTGTGGATCACGGA | ||
| varskip-0317-1_58_LEFT | CCAGCAACTGTTTGTGGACCTA | ||
| varskip-0317-1_58_RIGHT | TGGGTATGGCAATAGAGTTATTAGAGT | ||
| varskip-0317-1_59_LEFT | TGTGACATACCCATTGGTGCAG | ||
| varskip-0317-1_59_RIGHT | TTAAACTTTTGTGCACAAATGAGGTC | ||
| varskip-0317-1_60_LEFT | ACCAGATCCATCAAAACCAAGCA | ||
| varskip-0317-1_60_RIGHT | AATTTGCACTTCAGCCTCAACTT | ||
| varskip-0317-1_61_LEFT | TTCTTCCACAGCAAGTGCACTT | ||
| varskip-0317-1_61_RIGHT | ACAACATCACAGTTACCAGACACA | ||
| varskip-0317-1_62_LEFT | AACTGCTCCTGCCATTTGTCAT | ||
| varskip-0317-1_62_RIGHT | ACTGGCTCAGAGTCGTCTTCAT | ||
| varskip-0317-1_63_LEFT | GGAAAGTATGAGCAGTATATAAAATGGCC | ||
| varskip-0317-1_63_RIGHT | ACAAAGTTTATACTCTGCAAGAAGTAGAC | ||
| varskip-0317-1_64_LEFT | GCTTATTGTTGGCGTTGCACTT | ||
| varskip-0317-1_64_RIGHT | CGTCGATTGTGTGAATTTGGACA | ||
| varskip-0317-1_65_LEFT | GGAATCTGGAGTAAAAGACTGTGTT | ||
| varskip-0317-1_65_RIGHT | CATGGCTAAAATTAAAGTTCCAAACAGA | ||
| varskip-0317-1_66_LEFT | TGTGTGCGTACTGCTGCAATAT | ||
| varskip-0317-1_66_RIGHT | TTCTAGAAGCGGTCTGGTCAGA | ||
| varskip-0317-1_67_LEFT | TCTGGCTGTTATGGCCAGTAACT | ||
| varskip-0317-1_67_RIGHT | AAGATTCCAAATGGAAACTTTAAAAGTCC | ||
| varskip-0317-1_68_LEFT | TAGCAGGTGACTCAGGTTTTGC | ||
| varskip-0317-1_68_RIGHT | ACTTCCTCTTGTCTGATGAACAGT | ||
| varskip-0317-1_69_LEFT | AAAAGAACCTTGCTCTTCTGGAACAT | ||
| varskip-0317-1_69_RIGHT | GCACAATTCAATTAAAGGTGCTGAT | ||
| varskip-0317-1_70_LEFT | CTTTTGGTTCTCACTTGAACTGCA | ||
| varskip-0317-1_70_RIGHT | GGGGCCGACGTTGTTTTGAT | ||
| varskip-0317-1_71_LEFT | AGAGTATCATGACGTTCGTGTTGT | ||
| varskip-0317-1_71_RIGHT | CTCTGCTCCCTTCTGCGTAGAA | ||
| varskip-0317-1_72_LEFT | GCTGGACTTCCCTATGGTGCTA | ||
| varskip-0317-1_72_RIGHT | ACATTCCGAAGAACGCTGAAGC | ||
| varskip-0317-1_73_LEFT | GCCACTAAAGCATACAATGTAACACA | ||
| varskip-0317-1_73_RIGHT | Reverse | TTGTGCTATGTAGTTACGAGAATTCAT | |
| varskip-0317-1_74_LEFT | Forward | ACACAGGTGCCATCAAATTGGA | |
| varskip-0317-1_74_RIGHT | Reverse | GCACTACTAAAATTAATTTTACACATTAGGGC |