Primer Set: Hong Kong University

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{"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":"Hong Kong University","primer_set_name":"Hong_Kong_University","initial_lineage":"XFG","lineage_names":{"RV.1.1":"RV.1.1*","XFZ.4.1":"XFZ.4.1*","SW.2.1":"SW.2.1*","SJ":"SJ*","SW.2":"SW.2*","TA":"TA*","RK.1":"RK.1*","SV":"SV*","TA.1":"TA.1*","RW.1.1":"RW.1.1*","RV.2.1":"RV.2.1*","XFG.4":"XFG.4*","XFG.6":"XFG.6*","A":"A*","BA.2.86":"BA.2.86*","RF.5.4":"RF.5.4*","LF":"LF*","SW":"SW*","XFG.2":"XFG.2*","XFG":"XFG*","RF":"RF*","XFZ.4":"XFZ.4*","RV":"RV*","RF.5":"RF.5*","LP":"LP*","XFG.5":"XFG.5*","RK":"RK*","B":"B*","PG.3":"PG.3*","RW":"RW*","XFZ":"XFZ*","SV.1":"SV.1*","RV.1.3":"RV.1.3*","RE":"RE*","RW.1":"RW.1*","RV.1":"RV.1*","ST":"ST*","ST.1":"ST.1*","SJ.1":"SJ.1*","RE.2":"RE.2*","RV.2":"RV.2*","GW":"GW*","B.60":"B.60*","PQ.2":"PQ.2*","RE.1":"RE.1*","XFG.5.1":"XFG.5.1*","PG":"PG*","PG.3.2":"PG.3.2*","PQ":"PQ*","all":"All"},"variant_overlaps_path":"/organisms/sars-cov-2/lineage_variants/variant_overlaps.json"}

Lineage:

XFG* (1,637 in most recent 30 days)   └ XFG.6* (8 in most recent 30 days)   └ XFG.4*   └ XFG.2*   └ XFG.5*     └ XFG.5.1* XFZ* (306 in most recent 30 days)   └ XFZ.4* (52 in most recent 30 days)     └ XFZ.4.1* (52 in most recent 30 days) RV* (230 in most recent 30 days)   └ RV.1* (170 in most recent 30 days)     └ RV.1.3* (102 in most recent 30 days)     └ RV.1.1* (68 in most recent 30 days)   └ RV.2* (60 in most recent 30 days)     └ RV.2.1* (60 in most recent 30 days) SW* (166 in most recent 30 days)   └ SW.2* (166 in most recent 30 days)     └ SW.2.1* (166 in most recent 30 days) TA* (138 in most recent 30 days)   └ TA.1* (138 in most recent 30 days) RF* (135 in most recent 30 days)   └ RF.5* (135 in most recent 30 days)     └ RF.5.4* (65 in most recent 30 days) RW* (78 in most recent 30 days)   └ RW.1* (78 in most recent 30 days)     └ RW.1.1* (78 in most recent 30 days) ST* (58 in most recent 30 days)   └ ST.1* (58 in most recent 30 days) RK* (48 in most recent 30 days)   └ RK.1* (48 in most recent 30 days) SV* (47 in most recent 30 days)   └ SV.1* (20 in most recent 30 days) PQ*   └ PQ.2* PG*   └ PG.3*     └ PG.3.2* GW* RE*   └ RE.2*   └ RE.1* B*   └ B.60* LP* LF* BA.2.86* A* SJ*   └ SJ.1* All

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Primers:

Name	Locus	Category	Sequence
HKU-N-F	N	Forward	TAATCAGACAAGGAACTGATTA
HKU-N-P	N	Probe	GCAAATTGTGCAATTTGCGG
HKU-N-R	N	Reverse	CGAAGGTGTGACTTCCATG
HKU-ORF1b-nsp14-F	Orf1b	Forward	TGGGGYTTTACRGGTAACCT
HKU-ORF1b-nsp14-P	Orf1b	Probe	TAGTTGTGATGCWATCATGACTAG
HKU-ORF1b-nsp14-R	Orf1b	Reverse	AACRCGCTTAACAAAGCACTC

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