Fig. 1

Primer design for use in a tiling PCR assay for HIV-1 sequencing. A combination of published^30,31,32 and newly designed primers were utilised to amplify the 5’ end of HIV-1 in six 1 kb overlapping amplicons. Primers are split into two pools to ensure overlapping fragments are generated in separate reactions. Where a pan-subtype primer could not be designed, multiple subtype-specific primers were designed, targeting subtypes CRF01_AE, B and C as indicated. Blue highlighting in the genome indicates regions typically sequence for drug resistance screening.