Evidence of multiple introductions of HIV-1 subtype C in Angola

Infection, Genetics and Evolution

Volumn 12, Issue 7, 2012, Pages 1458-1465

  Afonso, Joana Morais ^a,b   Morgado, Mariza G ^a   Bello, Gonzalo ^a  

^a INSTITUTO OSWALDO CRUZ   (Brazil)

^b Universidade Agostinho Neto   (Angola)

Author keywords

Angola; HIV 1; Phylogeography; Subtype C

Indexed keywords

ADULT; ANGOLA; ANGOLAN; ARTICLE; BOTSWANA; BURUNDI; CLADISTICS; CLINICAL ARTICLE; CONGO; CONTROLLED STUDY; EPIDEMIC; ETHIOPIA; ETHNIC GROUP; EVOLUTION; FEMALE; GENE SEQUENCE; GEOGRAPHIC ORIGIN; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 1 SUBTYPE C; KENYA; MALAWI; MALE; MIGRATION; MOZAMBIQUE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PHYLOGENY; PHYLOGEOGRAPHY; PRIORITY JOURNAL; SAMPLE; SEQUENCE ANALYSIS; SOUTH AFRICA; TANZANIA; TIME; UGANDA; VIRUS STRAIN; ZAMBIA; ZIMBABWE;

ADULT; ANGOLA; BASE SEQUENCE; BAYES THEOREM; EPIDEMICS; EVOLUTION, MOLECULAR; FEMALE; HIV INFECTIONS; HIV-1; HUMANS; LIKELIHOOD FUNCTIONS; MALE; MIDDLE AGED; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; PHYLOGEOGRAPHY; SEQUENCE ANALYSIS, DNA; YOUNG ADULT;

EID: 84865386568     PISSN: 15671348     EISSN: 15677257     Source Type: Journal    
DOI: 10.1016/j.meegid.2012.05.005     Document Type: Article

References (25)

1. Abecasis A., Paraskevis D., Epalanga M., Fonseca M., Burity F., Bartolomeu J., Carvalho A.P., Gomes P., Vandamme A.M., Camacho R. HIV-1 genetic variants circulation in the North of Angola. Infect. Genet. Evol. 2005, 5:231-237.
2. Anisimova M., Gascuel O. Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative. Syst. Biol. 2006, 55:539-552.
3. Bartolo I., Epalanga M., Bartolomeu J., Fonseca M., Mendes A., Gama A., Taveira N. High genetic diversity of human immunodeficiency virus type 1 in Angola. AIDS Res. Hum. Retroviruses 2005, 21:306-310.
4. Bartolo I., Rocha C., Bartolomeu J., Gama A., Marcelino R., Fonseca M., Mendes A., Epalanga M., Silva P.C., Taveira N. Highly divergent subtypes and new recombinant forms prevail in the HIV/AIDS epidemic in Angola: new insights into the origins of the AIDS pandemic. Infect. Genet. Evol. 2009, 9:672-682.
5. Bello G., Afonso J.M., Morgado M.G. Phylodynamics of HIV-1 subtype F1 in Angola, Brazil and Romania. Infect. Genet. Evol. 2012, 12:1079-1086.
6. Bello G., Passaes C.P., Guimaraes M.L., Lorete R.S., Matos Almeida S.E., Medeiros R.M., Alencastro P.R., Morgado M.G. Origin and evolutionary history of HIV-1 subtype C in Brazil. AIDS 2008, 22:1993-2000.
7. Castelbranco E.P., da Silva Souza E., Cavalcanti A.M., Martins A.N., de Alencar L.C., Tanuri A. Frequency of primary resistance to antiretroviral drugs and genetic variability of HIV-1 among infected pregnant women recently diagnosed in Luanda-Angola. AIDS Res. Hum. Retroviruses 2010, 26:1313-1316.
8. Dalai S.C., de Oliveira T., Harkins G.W., Kassaye S.G., Lint J., Manasa J., Johnston E., Katzenstein D. Evolution and molecular epidemiology of subtype C HIV-1 in Zimbabwe. AIDS 2009, 23:2523-2532.
9. de Oliveira T., Deforche K., Cassol S., Salminen M., Paraskevis D., Seebregts C., Snoeck J., van Rensburg E.J., Wensing A.M., van de Vijver D.A., Boucher C.A., Camacho R., Vandamme A.M. An automated genotyping system for analysis of HIV-1 and other microbial sequences. Bioinformatics 2005, 21:3797-3800.
10. Drummond A.J., Ho S.Y., Phillips M.J., Rambaut A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 2006, 4:e88.
11. Drummond A.J., Nicholls G.K., Rodrigo A.G., Solomon W. Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 2002, 161:1307-1320.
12. Drummond A.J., Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 2007, 7:214.
13. Drummond A.J., Rambaut A., Shapiro B., Pybus O.G. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol. Biol. Evol. 2005, 22:1185-1192.
14. Guimaraes M.L., Vicente A.C., Otsuki K., da Silva R.F., Francisco M., da Silva F.G., Serrano D., Morgado M.G., Bello G. Close phylogenetic relationship between Angolan and Romanian HIV-1 subtype F1 isolates. Retrovirology 2009, 6:39.
15. Guindon S., Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 2003, 52:696-704.
16. Guindon S., Lethiec F., Duroux P., Gascuel O. PHYML online - a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res. 2005, 33:W557-559.
17. Hemelaar J., Gouws E., Ghys P.D., Osmanov S. Global trends in molecular epidemiology of HIV-1 during 2000-2007. AIDS 2011, 25:679-689.
18. Lemey P., Rambaut A., Drummond A.J., Suchard M.A. Bayesian phylogeography finds its roots. PLoS Comput. Biol. 2009, 5:e1000520.
19. Mehta S.R., Wertheim J.O., Delport W., Ene L., Tardei G., Duiculescu D., Pond S.L., Smith D.M. Using phylogeography to characterize the origins of the HIV-1 subtype F epidemic in Romania. Infect. Genet. Evol. 2011, 11:975-979.
20. Posada D. JModelTest: phylogenetic model averaging. Mol. Biol. Evol. 2008, 25:1253-1256.
21. Rambaut, A., 2009. FigTree v1.3.1: Tree Figure Drawing Tool. Available from http://tree.bio.ed.ac.uk/software/figtree/.
22. Rambaut, A., Drummond, A., 2007. Tracer v1.4. Available from http://beast.bio.ed.ac.uk/Tracer.
23. Rousseau C.M., Learn G.H., Bhattacharya T., Nickle D.C., Heckerman D., Chetty S., Brander C., Goulder P.J., Walker B.D., Kiepiela P., Korber B.T., Mullins J.I. Extensive intrasubtype recombination in South African human immunodeficiency virus type 1 subtype C infections. J. Virol. 2007, 81:4492-4500.
24. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The CLUSTAL_X windows interface. Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997, 25:4876-4882.
25. Vidal N., Peeters M., Mulanga-Kabeya C., Nzilambi N., Robertson D., Ilunga W., Sema H., Tshimanga K., Bongo B., Delaporte E. Unprecedented degree of human immunodeficiency virus type 1 (HIV-1) group M genetic diversity in the Democratic Republic of Congo suggests that the HIV-1 pandemic originated in Central Africa. J. Virol. 2000, 74:10498-10507.