High levels of discordance between sequencing and serological subtyping in a predominantly non-B subtype HIV-1 infected cohort

Samples from 457 randomly selected HIV-1 infected patients attending King's College Hospital were analysed using a subtype specific enzyme immunoassay. All serotyped non-Bs that provided unambiguous sequence and for which sufficient sample was available (n = 100), which included three serotyped subtype B samples were further analysed by env sequencing and subtyping using neighbour joining phylogenetic analysis, the NCB1 Retrovirus Genotyping too] and the Los Alamos BLAST search tool. Of the serotyped viruses, 45% (n = 204) samples were subtype B. Specifically serotyped non-B strains (n = 130) accounted for 28% of the total, of which the largest proportion were subtype C (n = 66). Twenty-seven samples (6%) were classified as non-B, 9% (n = 40) were multiply-reactive and 12% were non-reactive (n = 56). Of the 100 samples subtyped by sequencing the majority were subtype C (n = 32), followed by subtype A (n = 20). There was little concordance between the two methods. Although a 100% match was found among the serotyped and sequenced non-B viruses (n = 13), only 16 of the sequenced subtype C specimens matched the 29 obtained by serotyping. Of the 20 multi ply-reactive samples analysed by serotyping, only I sample consisted of a subtype mixture by sequencing. Of the 14 serologically non-reactive samples analysed, all were successfully sequenced, with subtype B strains (57%) the most common. Sequencing 15 samples in both env and pol regions revealed differences in subtype assignment for the same sample in some cases. Only 1/6 env subtype A and 4/5 env subtype C samples were concordant in pol sequence subtype. Differences were also found in subtyping by the different methods used. The overall agreement between the three methods was 89%. Four out of 11 samples agreed between the phylogenetic and Los Alamos methods, 1/11 between phylogenetic and BLAST and 2/11 between Los Alamos and BLAST. (C) 2004 Elsevier B.V. All rights reserved.