A pilot study was undertaken with the objective of developing a simple, eco
nomical, and efficient algorithm through which to subtype HIV-1 in a large
epidemiological cohort study in Uganda, A peptide enzyme immunoassay (PEIA)
employing both V3 and gp41 regions and a heteroduplex mobility assay (HMA)
were evaluated in comparison with DNA sequencing, Of 146 samples selected,
115 (79%) were successfully sequenced. Taking sequence data as the "gold s
tandard," other assays were compared with these data, The HMA correctly ide
ntified 95 (83%) of the samples, and only 1 sample was wrongly identified.
The V3 PEIA alone and in combination with gp41 peptides correctly identifie
d 76 and 78% of the samples, respectively; however, the number of wrongly i
dentified samples was four times less with the combination compared with V3
peptides alone (4 versus 16%). The sensitivity, specificity, and positive
and negative predictive values for serotype A and D samples were greater fo
r the combination than V3 peptides alone. We have described a new algorithm
to segregate subtypes A and D, This algorithm uses the two peptide assays
followed by HMA and then DNA sequencing for untypable samples, giving an ac
curacy of 95% at a cost of 37 and 21% for consumables compared with subtypi
ng all the samples by HMA or DNA sequencing, respectively. This proposed ap
proach is suitable for epidemiological studies in Uganda and other regions
with a predominance of A and D subtypes.