Increasing genetic distance to HIV-1 subtype B and F1 consensus sequences in the Brazilian epidemic: A challenge for vaccine strategies based on central immunogens?

Infection, Genetics and Evolution

Volumn 7, Issue 5, 2007, Pages 594-599

  Bello, Gonzalo ^a   Guimarães, Monick L ^a   Chequer Fernandez, Saada L ^a   Eyer Silva, Walter A ^a   Couto Fernandez, José C ^a   Teixeira, Sylvia L M ^a   Morgado, Mariza G ^a  

^a INSTITUTO OSWALDO CRUZ   (Brazil)

Author keywords

Brazil; Divergence; Diversity; HIV 1; Non synonymous; Subtype B; Subtype F1; Synonymous

Indexed keywords

AMINO ACID; HUMAN IMMUNODEFICIENCY VIRUS VACCINE; VIRUS ENVELOPE PROTEIN;

ARTICLE; BRAZIL; CONSENSUS SEQUENCE; CONTROLLED STUDY; EPIDEMIC; GENETIC DISTANCE; GENETIC VARIABILITY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; HUMAN IMMUNODEFICIENCY VIRUS INFECTED PATIENT; INTRASPECIFIC VARIATION; NONHUMAN; PRIORITY JOURNAL; SEQUENCE ANALYSIS; STRAIN DIFFERENCE; VIRUS ISOLATION; VIRUS STRAIN;

AIDS VACCINES; AMINO ACID SEQUENCE; BRAZIL; CONSENSUS SEQUENCE; DISEASE OUTBREAKS; DNA, VIRAL; GENE PRODUCTS, ENV; HIV INFECTIONS; HIV-1; HUMANS; VARIATION (GENETICS);

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 34548320983     PISSN: 15671348     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.meegid.2007.05.005     Document Type: Article

References (35)

1. Abascal F., Zardoya R., and Posada D. ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21 (2005) 2104-2105
2. Abebe A., Lukashov V.V., Pollakis G., Kliphuis A., Fontanet A.L., Goudsmit J., and de Wit T.F. Timing of the HIV-1 subtype C epidemic in Ethiopia based on early virus strains and subsequent virus diversification. AIDS 15 (2001) 1555-1561
3. Abebe A., Lukashov V.V., Rinke De Wit T.F., Fisseha B., Tegbaru B., Kliphuis A., Tesfaye G., Negassa H., Fontanet A.L., Goudsmit J., and Pollakis G. Timing of the introduction into Ethiopia of subcluster C′ of HIV type 1 subtype C. AIDS Res. Hum. Retroviruses 17 (2001) 657-661
4. Bello G., Eyer-Silva W.A., Couto-Fernandez J.C., Guimaraes M.L., Chequer-Fernandez S.L., Teixeira S.L., and Morgado M.G. Demographic history of HIV-1 subtypes B and F in Brazil. Infect. Genet. Evol. 7 (2007) 263-270
5. Bello G., Guimaraes M.L., and Morgado M.G. Evolutionary history of HIV-1 subtype B and F infections in Brazil. AIDS 20 (2006) 763-768
6. Foley B., Pan H., Buchbinder S., and Delwart E.L. Apparent founder effect during the early years of the San Francisco HIV type 1 epidemic (1978-1979). AIDS Res. Hum. Retroviruses 16 (2000) 1463-1469
7. Gaschen B., Taylor J., Yusim K., Foley B., Gao F., Lang D., Novitsky V., Haynes B., Hahn B.H., Bhattacharya T., and Korber B. Diversity considerations in HIV-1 vaccine selection. Science 296 (2002) 2354-2360
8. Grenfell B.T., Pybus O.G., Gog J.R., Wood J.L., Daly J.M., Mumford J.A., and Holmes E.C. Unifying the epidemiological and evolutionary dynamics of pathogens. Science 303 (2004) 327-332
9. Jones D.T., Taylor W.R., and Thornton J.M. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8 (1992) 275-282
10. Korber B., Gaschen B., Yusim K., Thakallapally R., Kesmir C., and Detours V. Evolutionary and immunological implications of contemporary HIV-1 variation. Br. Med. Bull. 58 (2001) 19-42
11. Korber B., Muldoon M., Theiler J., Gao F., Gupta R., Lapedes A., Hahn B.H., Wolinsky S., and Bhattacharya T. Timing the ancestor of the HIV-1 pandemic strains. Science 288 (2000) 1789-1796
12. Korber B., Theiler J., and Wolinsky S. Limitations of a molecular clock applied to considerations of the origin of HIV-1. Science 280 (1998) 1868-1871
13. Kuiken C.L., Lukashov V.V., Baan E., Dekker J., Leunissen J.A., and Goudsmit J. Evidence for limited within-person evolution of the V3 domain of the HIV-1 envelope in the Amsterdam population. AIDS 10 (1996) 31-37
14. Kuiken C.L., Zwart G., Baan E., Coutinho R.A., van den Hoek J.A., and Goudsmit J. Increasing antigenic and genetic diversity of the V3 variable domain of the human immunodeficiency virus envelope protein in the course of the AIDS epidemic. Proc. Natl. Acad. Sci. U.S.A. 90 (1993) 9061-9065
15. Kumar S., Tamura K., and Nei M. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform. 5 (2004) 150-163
16. Li W.H. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36 (1993) 96-99
17. Lukashov V.V., and Goudsmit J. Evolution of the human immunodeficiency virus type 1 subtype-specific V3 domain is confined to a sequence space with a fixed distance to the subtype consensus. J. Virol. 71 (1997) 6332-6338
18. Lukashov V.V., and Goudsmit J. Recent evolutionary history of human immunodeficiency virus type 1 subtype B: reconstruction of epidemic onset based on sequence distances to the common ancestor. J. Mol. Evol. 54 (2002) 680-691
19. Morgado M.G., Guimaraes M.L., and Galvao-Castro B. HIV-1 polymorphism: a challenge for vaccine development-a review. Mem. Inst. Oswaldo Cruz 97 (2002) 143-150
20. Murphy E., Korber B., Georges-Courbot M.C., You B., Pinter A., Cook D., Kieny M.P., Georges A., Mathiot C., Barre-Sinoussi F., et al. Diversity of V3 region sequences of human immunodeficiency viruses type 1 from the central African Republic. AIDS Res. Hum. Retroviruses 9 (1993) 997-1006
21. Nabel G., Makgoba W., and Esparza J. HIV-1 diversity and vaccine development. Science 296 (2002) 2335
22. Nickle D.C., Jensen M.A., Gottlieb G.S., Shriner D., Learn G.H., Rodrigo A.G., and Mullins J.I. Consensus and ancestral state HIV vaccines. Science 299 (2003) 1515-1518 (author reply 1515-1518)
23. Novitsky V., Smith U.R., Gilbert P., McLane M.F., Chigwedere P., Williamson C., Ndung'u T., Klein I., Chang S.Y., Peter T., Thior I., Foley B.T., Gaolekwe S., Rybak N., Gaseitsiwe S., Vannberg F., Marlink R., Lee T.H., and Essex M. Human immunodeficiency virus type 1 subtype C molecular phylogeny: consensus sequence for an AIDS vaccine design?. J. Virol. 76 (2002) 5435-5451
24. Pamilo P., and Bianchi N.O. Evolution of the Zfx and Zfy genes: rates and interdependence between the genes. Mol. Biol. Evol. 10 (1993) 271-281
25. Posada D., and Crandall K.A. MODELTEST: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
26. Robbins K.E., Lemey P., Pybus O.G., Jaffe H.W., Youngpairoj A.S., Brown T.M., Salemi M., Vandamme A.M., and Kalish M.L. U.S. Human immunodeficiency virus type 1 epidemic: date of origin, population history, and characterization of early strains. J. Virol. 77 (2003) 6359-6366
27. Salemi M., Strimmer K., Hall W.W., Duffy M., Delaporte E., Mboup S., Peeters M., and Vandamme A.M. Dating the common ancestor of SIVcpz and HIV-1 group M and the origin of HIV-1 subtypes using a new method to uncover clock-like molecular evolution. FASEB J. 15 (2001) 276-278
28. Sharp P.M., Bailes E., Chaudhuri R.R., Rodenburg C.M., Santiago M.O., and Hahn B.H. The origins of acquired immune deficiency syndrome viruses: where and when?. Phil. Trans. R. Soc. Lond. B: Biol. Sci. 356 (2001) 867-876
29. Tamura K., and Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10 (1993) 512-526
30. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 (1997) 4876-4882
31. Travers S.A., Clewley J.P., Glynn J.R., Fine P.E., Crampin A.C., Sibande F., Mulawa D., McInerney J.O., and McCormack G.P. Timing and reconstruction of the most recent common ancestor of the subtype C clade of human immunodeficiency virus type 1. J. Virol. 78 (2004) 10501-10506
32. Triques K., Bourgeois A., Saragosti S., Vidal N., Mpoudi-Ngole E., Nzilambi N., Apetrei C., Ekwalanga M., Delaporte E., and Peeters M. High diversity of HIV-1 subtype F strains in Central Africa. Virology 259 (1999) 99-109
33. Van de Peer Y., Janssens W., Heyndrickx L., Fransen K., van der Groen G., and De Wachter R. Phylogenetic analysis of the env gene of HIV-1 isolates taking into account individual nucleotide substitution rates. AIDS 10 (1996) 1485-1494
34. Vidal N., Peeters M., Mulanga-Kabeya C., Nzilambi N., Robertson D., Ilunga W., Sema H., Tshimanga K., Bongo B., and 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. 74 (2000) 10498-10507
35. Yusim K., Peeters M., Pybus O.G., Bhattacharya T., Delaporte E., Mulanga C., Muldoon M., Theiler J., and Korber B. Using human immunodeficiency virus type 1 sequences to infer historical features of the acquired immune deficiency syndrome epidemic and human immunodeficiency virus evolution. Phil. Trans. R. Soc. Lond. B: Biol. Sci. 356 (2001) 855-866