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Table 5 Suggested primer stretches (for sequencing and PCR) based on HCV whole genome PWM for analyzing signature nucleotides selected for NS5B and E1 region.

From: HCV genotyping using statistical classification approach

 

Forward Primers

Reverse Primers

 

Start

End

Conservation Score (%)

Sequence

Start

End

Conservation Score (%)

Sequence

NS5B

8050

8074

93.2

AGCCAGCTCGCCTTATCGTATTCCC

8629

8605

94.5

GCGGAATACCTGGTCATAGCCTCCG

 

8083

8107

89.1

GGGTTCGTGTGTGCGAGAAGATGGC

8800

8776

91.1

ACTGGAGTGTGTCTAGCTGTCTCCC

 

8082

8106

89.0

GGGGTTCGTGTGTGCGAGAAGATGG

8634

8610

89.7

GGGGGGCGGAATACCTGGTCATAGC

 

8125

8149

85.9

CCACCCTTCCTCAGGCCGTGATGGG

8633

8609

89.7

GGGGGCGGAATACCTGGTCATAGCC

 

8124

8148

84.3

TCCACCCTTCCTCAGGCCGTGATGG

    

E1

709

733

94.1

CATGCGGCTTCGCCGACCTCATGGG

1612

1588

89.3

TTCAGGGCAGTCCTGTTGATGTGCC

 

708

732

94.0

ACATGCGGCTTCGCCGACCTCATGG

1605

1581

89.3

CAGTCCTGTTGATGTGCCAGCTGCC

 

733

757

93.0

GGTACATTCCGCTCGTCGGCGCCCC

1629

1605

83.2

TGAGGCTGTCATTGCAGTTCAGGGC

 

821

845

91.2

TGCAACAGGGAACCTTCCTGGTTGC

    
  1. To ensure optimal polymerization, the 3' end and the penultimate position were required to be G or C with frequencies of ≥0.98 and the upstream position, (3' -2), a G or C with a frequency of ≥0.90 or alternatively an A or T with a frequency of ≥0.95.