. Author manuscript; available in PMC: 2023 May 22.

Published in final edited form as: Nat Microbiol. 2023 Jan 30;8(2):260–271. doi: 10.1038/s41564-022-01306-6

Extended Data Table 3.

Amplification and sequencing primers

Primer	Sequence
SGA1 Forward	TGCCAAGAAAAGCAAAGATCATTAG
SGA1 Reverse	GACTCTCGAGAAGCACTCAAGGCAAGCTTTATTGAG
SGA2 Forward	GATCAAGCTTTAGGCATCTCCTATGGCAGGAAGAAG
SGA2 Reverse	GACTCTCGAGAAGCACTCAAGGCAAGCTTTATTGAG
MiSeq Subtype B V3 cDNA^*	GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNCAGTCCATTTTGCTYTAYTRABVTTACAATRTGC
MiSeq Subtype C V3 cDNA^*	GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNGCTATGTGTTGTAATTTCTAGGTCCCCT
MiSeq PR cDNA^*	GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNCAGTTTAACTTTTGGGCCATCCATTCC
MiSeq IN cDNA^*	GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNATCGAATACTGCCATTTGTACTGC
MiSeq RT cDNA^*	GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNCAGTCACTATAGGCTGTACTGTCCATTTATC
MiSeq V3 PCR1	GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNTTATGGGATCAAAGCCTAAAGCCATGTGTA
MiSeq PR PCR1	GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNTCAGAGCAGACCAGAGCCAACAGCCCCA
MiSeq IN PCR1	GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNAAAAGGAGAAGCCATGCATG
MiSeq RT PCR1	GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNGGCCATTGACAGAAGAAAAAATAAAAGC
MiSeq PCR1 reverse primer	GTGACTGGAGTTCAGACGTGTGCTC
MiSeq PCR2 primer 1	AATGATACGGCGACCACCGAGATCTACACGCCTCCCTCGCGCCATCAGAGATGTG
MiSeq PCR2 primer 2^**	CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGTGCTC
Sequencing primer for MiSeq runs	GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAG

Primers used to amplify and sequence HIV-1 RNA for both Illumina MiSeq with Primer ID and single genome amplification (SGA).

Ns in the cDNA primer sequences are random primers

^**

In the index primer the 6-N is not a random primer but a pre-designed index sequence. We use a set of 24 indices