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.



ML Radial Phylogenetic Tree Subtype C (26 complete genomes)

ML Phylogram Phylogenetic Tree Subtype C (26 complete genomes)

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)


References


1. Soares MA, de Oliveira T, Brindeiro RM, Diaz RS, Sabino EC,  Brigido L, Pires IL, Morgado MC, Dantas MC, Barreira D, Teixeira PR, Cassol S, Tanuri A. 2003. A specific subtype C of human immunodeficiency virus type 1 circulates in Brazil. AIDS 17: 11-21. [Medline]

2. Shankarappa R, Chatterjee R, Learn GH, Neogi D, Ding M, Roy P, Ghosh A, Kingsley L, Harrison L, Mullins JI, Gupta P. 2001. Human immunodeficiency virus type 1 env sequences from Calcutta in eastern India: Identification of features that distinguish subtype C sequences in India from other subtype C sequences. J Virology 75 (21): 10479-10487. [Medline]

3. Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, Novak NG, Ingersoll R, Sheppard HW, Ray SC. 1999. Full-length human immunodeficiency virus type 1 genomes from subtype C infected seroconverters in India, with evidence of intersubtype recombination. J Virology. 73 (1): 152-60. [Medline]

4. Novitsky VA, Montano MA, McLane MF, Renjifo B, Vannberg FA, Foley BT, Ndung'u TP, Rahman M, Makhema MJ, Marlink R, Essex M. 1999. Molecular cloning and phylogenetic analysis of human immunodeficiency virus type 1 subtype C: a set of 23 full-length clones from Botswana. J Virology 73 (5): 4427-32. [Medline]

5. Salminen MO, Johansson B, Sonnerborg A, Ayehunnie S, Gotte D, Leinikki P, Burke DS, McCutchan FE. 1996. Full-length sequence of an Ethiopian human immunodeficiency virus type 1 (HIV-1) isolate of genetic subtype C. AiDS Res Hum Retroviruses. 12: 1329-39. [Medline]

6. Rodenburg CM, Li Y, Trask SA, Chen Y, Decker J, Robertson DL, Kalish ML, Shaw GM, Allen S, Hahn BH, Gao F, UNAIDS and NIAID networks for HIV isolation and characterization. 2001. Near full-length clones and reference sequences for subtype C isolates of HIV type 1 from three diffent continents. AIDS Res Hum Retroviruses. 17 (2): 161-68. [Medline]

7. zur Megede J, Engelbrecht S, de Oliveira T, Cassol S, Scriba TJ, Janse van Rensburg E, Barnett SW. 2002. Novel evolutionary analyses of full-length HIV type 1 subtype C molecular clones from Cape Town,South Africa. AIDS Res Hum Retroviruses. 18 (17): 1327-32. [Medline]

8. van Harmelen J, Williamson C, Kim B, Morris L, Carr J, Abdool Karim SS, McCutchan F. 2001. Characterization of full-length HIV type 1 subtype C sequences from South Africa. AIDS Res Hum Retroviruses. 17 (16): 1527-31. [Medline]

9. Papathanasopoulos MA, Cilliers T, Morris L, Mokili JL, Dowling W, Birx DL, McCuthan FE. 2002. Full-length genome analysis of HIV-1 subtype C utilizing CXCR4 and intersubtype recombinants isolated in South Africa. AIDS Res Hum Retroviruses. 18 (12): 879-86. [Medline]

10. Kaplan EH, Kedem E, Pollack S. 1998. HIV incidence in Ethiopian immigrants to Israel. J Acquir Immune Defic Syndr Hum Retrovirol. 17 (5):465-9 [Medline]


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