Phylogenetic trees of HIV-1 subtype C complete genome sequences:

This section presents maximum likelihood (ML) and neighbour-joininig (NJ) phylogenetic trees of two reference datasets of hiv-1 subtype c. These datasets contains 116 and 26 reference complete genome sequences where the country of isolation is identified.

Figure Legend: A phylogenetic tree of 26 HIV-1 subtype C sequences. Complete genome sequences of subtype C from Brazil (2), Botswana (5), India (5), Ethiopia (1), Israel (1), South Africa (5), Tanzania (4), Zambia (2) and Kenya (1) were collected from LANL and used for phylogenetic analysis. The sequences were aligned in Clustal X and a neighbour-joining tree constructed in PAUP*, where also the bootstrap analysis was carried out. A thousand (1000) reps were carried out on the neighbour-joining tree for the bootstrap analysis. Bootstrap values less than 80% are not shown on the tree. Only sequences from Brazil (BR) and India (IN) formed country-specific clusters (monophyletic groups) indicating a founder-effect of the subtype C virus in these countries. The same monophyletic clusters were lso evident when sub-genomic regions of sequences from these two countries were phylogenetically analyzed in the same way (1, Gordon et al, 2003). In contrast, the sequences from the African countries do no exhibit country-specific clusters and instead show a random spread of the sequence throughout the tree indicating multiple introduction of subtype C viruses in these countries. The clustering of sequences from Israel (IS)and Ethiopia (ETH)indicate that the two sequences are related and are supported by epidemiological data that suggested that subtype C in Israel may have beeen introduced from Ethiopia (10).

NJ Radial Phylogenetic Tree Subtype C (116 complete genomes)

Phylogenetic tree of 116 HIV-1 subtype C complete genomes.   Complete genome sequences of subtype C from Brazil (2), Botswana (53), India (11), Ethiopia (7), Israel (1), South Africa (37), Tanzania (4), Zambia (2) and Kenya (1) were collected from LANL and used for phylogenetic analysis. The sequences are described in a table in (html) and (text) format. Only sequences from Brazil (BR) and India (IN) formed country-specific clusters (monophyletic groups) indicating a founder-effect of the subtype C virus in these countries (ref 1, 2). The same monophyletic clusters were also evident when sub-genomic regions of sequences from these two countries were phylogenetically analyzed in the same way or when fewer sequences were used (below). The sequences from the African countries do not exhibit country-specific clusters and instead show a spread of the sequences throughout the tree indicating multiple introductions of subtype C viruses in these countries. South Africa and Botswana show some specific lineages, although the large sample size can have an influence on the distribution of the sequences in the tree (ref 4, 7, 8, 9). The clustering of sequences from Israel and Ethiopia indicate that the two sequences are related and are supported by epidemiological data suggesting that subtype C in Israel may have been introduced from Ethiopia.(ref 5, 10)