Table 1 Overview of primers and probes for the subtype B&C IPDA

psi forward

TCTCGACGCAGGACTCG

684–700

psi probe

/56-FAM/CTCTCTCCT/ZEN/TCTAGCCTC/3IABkFQ/

772–789

psi reverse subtype B

TACTGACGCTCTCGCACC

793–810

psi reverse subtype C

TATTGACGCTCTCGCACC

793–810

env forward subtype B

AGTGGTGCAGAGAGAAAAAAGAGC

7736–7759

env forward subtype C

AGTGGTGGAGAGAGAAAAAAGAGC

7736–7759

env probe

/5HEX/CCTTGGGTT/ZEN/CTTGGGAGC/3IABkFQ/

7781–7798

env hypermutation probe

/5IABkFQ/CCTTAGGTTCTTAGGAGC/3IABkFQ/

7781–7798

env reverse

GTCTGGCCTGTACCGTCAGC

7851–7832

RPP30 forward 1

GATTTGGACCTGCGAGCG

n/a

RPP30 reverse 1

GCGGCTGTCTCCACAAGT

n/a

RPP30 probe

/5HEX/CTGACCTGA/ZEN/AGGCTCT/3IABkFQ/

n/a

RPP30 forward 2

CCATTTGCTGCTCCTTGGG

n/a

RPP30 reverse 2

CATGCAAAGGAGGAAGCCG

n/a

RPP30 probe 2

/56-FAM/AAGGAGCAA/ZEN/GGTTCTATTGTAG/3IABkFQ/

n/a