Analysis of a new subtype of HIV-1 gag sequence from a case of vertical transmission in Taiwan.

A Taiwanese woman who lived with a presumably bisexual man of German nationality, and her infant daughter were found to be seropositive for HIV-1. From DNA preparations of peripheral blood mononuclear cells of the mother-infant pair, we amplified a segment, about 560 base pairs (bp), of gag portion of HIV-1 provirus by using polymerase chain reaction (PCR). The high degree of homology (94.7-97.5%) among clones (TM-1 and TM-2 from the mother, and TC-1 and TC-2 from the infant) of gag sequence provided a molecular epidemiological evidence for vertical transmission. However, these sequences exhibited lower degrees of homology (85.1-87.0%) with the corresponding gag segment of a North American HIV-1 subtype (HXB2), and that of a Zairean HIV-1 subtype (Z2Z6). The disparity of sequences between these Taiwanese clones and those of HXB2 and Z2Z6 was particularly prominent in the first (5' proximal) 200 bp, as shown by the low degree of homology (74.8-79.6%) when sequences of TM and TC clones which represented the first 200 bp were compared with those of HXB2 and Z2Z6. The sequence dissimilarity of these clones as compared with HXB2 manifested as transitions more frequently than transversions. Transitions involving G/A to A/G changes were more frequent than those involving T/C to C/T. Transversions involving G/A to T/C changes were slightly more frequent than those involving T/C to G/A changes for all clones except for TM-2 which showed an equal frequency. Presence of stop codons in each of the reading frames of these clones suggests that these may represent defective viral quasispecies. The deduced amino acid sequences from available open reading frames of these clones showed also distinct dissimilarities to HXB2 or Z2Z6. These findings indicate the presence of a gag subtype of HIV-1 which, according to the phylogenetic tree analysis, would represent a new subtype distinct from other known subtypes.