Also, when using gene fragments, occasionally sequences may not give clear cut answers over short stretches. However, phylogenetic analyses of V3 sequences on occasion produce trees that show a close accosiation of subtype H and A sequences. Since this discordance is not always observed but depends on the particular alignments and programs used, it is not sufficient evidence for recombination. Nevertheless, the fact that it can occur, underscores the possbility of ambiguities that can arise with subtyping efforts, particularly those directed at short regions of the genome. All of the longer subtype G sequences available to date have stretches of subtype A-associated sequence interspersed.
Further analysis is necessary to determine the potential they have to represent a distinct subtype.
However, these sequences are included as reference sequences to assist in identification of possible J subtype related strains in the future. Table 1A. Updated Proposal of Reference Sequences of HIV-1 Genetic Subtypes. The alignments for the various subgenomic regions are derived from the complete genomic alignment, as presented in the HIV database 1997. Although G subtype sequences in the trees shown cluster seperate from subtype A, they cluster in Subtype A in some subgene regions 6 . Subtypes B and D are generally close to each other in all analyses, but with nef gene it may be difficult to completely resolve them from each other.