Skip to main content

Advertisement

Table 2 Sequences of primers and probes in the direction 5’-3’

From: Hepatitis A virus subgenotyping based on RT-qPCR assays

Genotype Reference strain   Sequence Position
HAV IA AB020564.1 Forward primer GCA TTT AGG TTT TTC CTC ATT 702-722
Reverse primer TCA ACK GAC TGA ATC ATT 837-820
Probe TCC AAA CAA GGA ATT TTC CAG AC 743-765
HAV IB M14707 Forward primer AAG CTT ATT GTG TAY TGT TAT 2070-2090
Reverse primer CAG AAT CAT CTC CAA CYT 2223-2208
Probe TTC TCC TTC TAA C GT TGC TTC CCA 2103-2125
HAV IIA AY644676.1 Forward primer ACY ATG ATG AGC AGA ATT G 2978-2996
Reverse primer GCA TAT TTT AAT CTC TGC TT 3129-3110
Probe AGA CCT GGA ATC G TC AGT GGA TGA 3004-3027
HAV IIB AY644670.1 Forward primer GGA GAT TTG AAA GTC ATA TTG 3047-3067
Reverse primer TTC CTG GGC ATA CTT TAG 3135-3118
Probe AGT CTT AAT TCT TTG TAT GGT TTTC 3078-3094
HAV IIIA AB279732.1 Forward primer TCC CTT GGA TTT GAC AAT 2605-2622
Reverse primer RGT ATT RAA CCT AAC AGC 2763-2747
Probe AAT TAT AAC TGG G GC TAC TGA TGT T 2623-2647
HAV IIIB AB279735.1 Forward primer AAT CCG ATG CTT CTC AAG 1560-1577
Reverse primer GCC TTC CTG AAT GGT ATT 1841-1824
Probe AAA ATT ACA CAC TTY ACA ACY TGG A 1589-1613
HAV 5’UTR M14707 Forward primer* TCA CCG CCG TTT GCC TAG 68-85
Reverse primer* GGA GAG CCC TGG AAG AAA G 241-223
Probe* CCT GAA CCT GCA GGA ATT AA 169-150
  1. The specific genotype SNP is in bold. Probes are FAM-BHQ except HAV 5’UTR which is FAM-MGB. *: Costafreda et al. [19].