Phylogenetic analysis of 49 newly derived HIV-1 group O strains: High viral diversity but no group M-like subtype structure

Virology

Volumn 302, Issue 2, 2002, Pages 259-273

  Roques, P ^a,d   Robertson, D L ^b   Souquiere S ^d   Damond, F ^c   Ayouba, A ^e   Farfara, I ^c   Depienne, C ^a   Nerrienet, E ^e   Dormont, D ^a   Brun Vezinet F ^c   Simon, F ^c,d   Mauclere P ^e,f  

^a INSTITUT DE RADIOPROTECTION ET DE SÛRETÉ NUCLÉAIRE   (France)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c BICHAT HOSPITAL   (France)

^d CENTRE INTERNATIONAL DE RECHERCHES MÉDICALES DE FRANCEVILLE   (Gabon)

^e CENTRE PASTEUR DU CAMEROUN   (Cameroon)

^f INSTITUT PASTEUR DE MADAGASCAR   (Madagascar)

Author keywords

Cameroon, France; Diversity; Group O; HIV; Molecular epidemiology; Phylogeny

Indexed keywords

ADULT; AGED; ARTICLE; CLINICAL ARTICLE; CONTROLLED STUDY; FEMALE; FRANCE; GENE CLUSTER; GENE IDENTIFICATION; GENE SEQUENCE; HUMAN; HUMAN CELL; HUMAN IMMUNODEFICIENCY VIRUS 1; INFANT; MALE; MICROBIAL DIVERSITY; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; STRAIN DIFFERENCE; VIRAL GENETICS; VIRUS GENOME;

HUMAN IMMUNODEFICIENCY VIRUS 1; PUFFINUS AURICULARIS;

EID: 0036436724     PISSN: 00426822     EISSN: None     Source Type: Journal    
DOI: 10.1006/viro.2002.1430     Document Type: Article

References (55)

1. Ayouba, A., Mauclere, P., Martin, P., Cunin, P., Mfoupouendoun, J., Njinku, B., Souquiere, S., and Simon, F. (2001). Stability of HIV-1 group-0 infection in Cameroon over a twelve years period. Emerg. Infect. Dis. 7, 466-467.
2. Ayouba, A., Souquiere, S., Njinku, B., Martin, P., Muller-Trutwin, M. C., Roques, P., Barre-Sinoussi, F., Mauclere, P., Simon, F., and Nerrienet, E. (2000). HIV-1 group N among HIV-1 seropositive individuals in Cameroon. AIDS 14, 2623-2625.
3. Bibollet-Ruche, F., Loussert-Ajaka, I., Simon, F., Mboup, S., Ngole, E. M., Saman, E., Delaporte, E., and Peeters, M. (1998). Genetic characterization of accessory genes from human immunodeficiency virus type 1 group O strains. AIDS Res. Hum. Retroviruses 14, 951-961.
4. Bibollet-Ruche, F., Peeters, M., Mboup, S., Ekaza, E., Gandji, R., Torimiro, J., Mpoudi, E. N., Amblard, J., Dibanga, G., Saidou, M., Esu-Williams, E., Vanden Haesevelde, M., Saman, E., and Delaporte, E. (1998). Molecular characterization of the envelope transmembrane glycoprotein of 13 new human immunodeficiency virus type 1 group O strains from six different African countries. AIDS Res. Hum. Retroviruses 14, 1281-1285.
5. Braaten, D., Franke, E. K., and Luban, J. (1996). Cyclophilin A is required for the replication of group M human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency virus SIV(CPZ)GAB but not group O HIV-1 or other primate immunodeficiency viruses. J. Virol. 70, 4220-4227.
6. Chaix-Baudier, M. L., Chappey, C., Burgard, M., Letourneur, F., Igual, J., Saragosti, S., and Rouzioux, C. (1998). First case of mother-to-infant HIV type 1 group O transmission and evolution of C2V3 sequences in the infected child. French HIV Pediatric Cohort Study Group. AIDS Res. Hum. Retroviruses 14, 15-23.
7. Charneau, P., Borman, A. M., Quillent, C., Guetard, D., Chamaret, S., Cohen, J., Remy, G., Montagnier, L., and Clavel, F. (1994). Isolation and envelope sequence of a highly divergent HIV-1 isolate: Definition of a new HIV-1 group. Virology 205, 247-253.
8. Corbet, S., Muller-Trutwin, M. C., Versmisse, P., Delarue, S., Ayouba, A., Lewis, J., Brunak, S., Martin, P., Brun-Vezinet, F., Simon, F., Barre-Sinoussi, F., and Mauclere, P. (2000). env sequences of simian immunodeficiency viruses from chimpanzees in Cameroon are strongly related to those of human immunodeficiency virus group N from the same geographic area. J. Virol. 74, 529-534.
9. De Leys, R., Vanderborght, B., Vanden Haesevelde, M., Heyndrickx, L., van Geel, A., Wauters, C., Bernaerts, R., Saman, E., Nijs, P., Willems, B., et al. (1990). Isolation and partial characterization of an unusual human immunodeficiency retrovirus from two persons of west-central African origin. J. Virol. 64, 1207-1216.
10. Dorn, J., Masciotra, S., Yang, C., Downing, R., Biryahwaho, B., Mastro, T. D., Nkengasong, J., Pieniazek, D., Rayfield, M. A., Hu, D. J., and Lal, R. B. (2000). Analysis of genetic variability within the immunodominant epitopes of envelope gp41 from HIV-1 group M and its impact on HIV-1 antibody detection. J. Clin. Microbiol. 38, 773-780.
11. Gao, F., Bailes, E., Robertson, D. L., Chen, Y., Rodenburg, C. M., Michael, S. F., Cummins, L. B., Arthur, L. O., Peeters, M., Shaw, G. M., Sharp, P. M., and Hahn, B. H. (1999). Origin of HIV-1 in the chimpanzee Pan troglodytes troglodytes. Nature 397, 436-441.
12. Gurtler, L. G., Hauser, P. H., Eberle, J., von Brunn, A., Knapp, S., Zekeng, L., Tsague, J. M., and Kaptue, L. (1994). A new subtype of human immunodeficiency virus type 1 (MVP-5180) from Cameroon. J. Virol. 68, 1581-1585.
13. Hackett, J., Jr., Zekeng, L., Brennan, C. A., Lund, J. K., Vallari, A. S., Hickman, R. K., Gurtler, L., Kaptue, L., and Devare, S. G. (1997). Genetic analysis of HIV type 1 group O p24 gag sequences from Cameroon and Equatorial Guinea. AIDS Res. Hum. Retroviruses 13, 1155-1158.
14. Hampl, H., Sawitzky, D., Stoffler-Meilicke, M., Groh, A., Schmitt, M., Eberle, J., and Gurtler, L. (1995). First case of HIV-1 subtype 0 infection in Germany. Infection 23, 369-370.
15. Hasegawa, M., Kishino, H., and Yano, T. (1985). Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22, 160-174.
16. Heyndrickx, L., Alary, M., Janssens, W., Davo, N., and van der Groen, G. (1996). HIV-1 group O and group M dual infection in Benin. Lancet 347, 902-903.
17. Hunt, J. C., Brennan, C. A., Golden, A. M., Yamaguchi, J., Lund, J. K., Vallari, A. S., Hickman, R. K., Zekeng, L., Gurtler, L. G., Hampl, H., Kaptue, L., and Devare, S. G. (1997). Molecular analyses of HIV-1 group O and HIV-2 variants from Africa. Leukemia 3, 138-141.
18. Hunt, J. C., Golden, A. M., Lund, J. K., Gurtler, L. G., Zekeng, L., Obiang, J., Kaptue, L., Hampl, H., Vallari, A., and Devare, S. G. (1997). Envelope sequence variability and serologic characterization of HIV type 1 group O isolates from equatorial guinea. AIDS Res. Hum. Retroviruses 13, 995-1005.
19. Janssens, W., Heyndrickx, L., Van der Auwera, G., Nkengasong, J., Beirnaert, E., Vereecken, K., Coppens, S., Willems, B., Fransen, K., Peeters, M., Ndumbe, P., Delaporte, E., and van der Groen, G. (1999). Interpatient genetic variability of HIV-1 group O. AIDS 13, 41-48.
20. Jonassen, T. O., Stene-Johansen, K., Berg, E. S., Hungnes, O., Lindboe, C. F., Froland, S. S., and Grinde, B. (1997). Sequence analysis of HIV-1 group O from Norwegian patients infected in the 1960s. Virology 231, 43-47.
21. Kabeya, C. M., Esu-Williams, E., Eni, E., Peeters, M., Saman, E., and Delaporte, E. (1995). Evidence for HIV-1 group O infection in Nigeria. Lancet 346, 308.
22. Kane, C., Montavon, C., Toure, M., Faye, M., Ndiaye, A., Diallo, A., I. N., Liegeois, F., Delaporte, E., Mboup, S., and Peeters, M. (2001). Full-length genome sequencing of HIV-1 group O viruses isolated from a heterosexual transmission cluster in senegal. AIDS Res. Hum. Retroviruses 17, 1167-1173.
23. Korber, B., Muldoon, M., Theiler, J., Gao, F., Gupta, R., Lapedes, A., Hahn, B. H., Wolinsky, S., and Bhattacharya, T. (2000). Timing the ancestor of the HIV-1 pandemic strains. Science 288, 1789-1796.
24. Loussert-Ajaka, I., Chaix, M. L., Korber, B., Letourneur, F., Gomas, E., Allen, E., Ly, T. D., Brun-Vezinet, F., Simon, F., and Saragosti, S. (1995). Variability of human immunodeficiency virus type 1 group O strains isolated from Cameroonian patients living in France. J. Virol. 69, 5640-5649.
25. Loussert-Ajaka, I., Ly, T. D., Chaix, M. L., Ingrand, D., Saragosti, S., Courouce, A. M., Brun-Vezinet, F., and Simon, F. (1994). HIV-1/HIV-2 seronegativity in HIV-1 subtype O infected patients. Lancet 343, 1393-1394.
26. Mammano, F., Öhagen, A., Höglund, S., and Göttlinger, H. G. (1994). Role of the major homology region of HIV-1 in virion morphogenesis. J. Virol. 68, 4927-4936.
27. Mas, A., Quinones-Mateu, E., Soriano, V., and Domingo, E. (1996). Env gene characterization of the first HIV type 1 group O Spanish isolate. AIDS Res. Hum. Retroviruses 12, 1647-1649.
28. Mas, A., Quinones-Mateu, M. E., Domingo, E., and Soriano, V. (1999). Phylogeny of HIV type 1 group O isolates based on env gene sequences. AIDS Res. Hum. Retroviruses 15, 769-773.
29. Mauclere, P., Damond, F., Apetrei, C., Loussert-Ajaka, I., Souquiere, S., Buzelay, L., Dalbon, P., Jolivet, M., Mony Lobe, M., Brun-Vezinet, F., Simon, F., and Barin, F. (1997). Synthetic peptide ELISAs for detection of and discrimination between group M and group O HIV type 1 infection. AIDS Res. Hum. Retroviruses 13, 987-993.
30. Mauclere, P., Loussert-Ajaka, I., Damond, F., Fagot, P., Souquieres, S., Monny Lobe, M., Mbopi Keou, F. X., Barre-Sinoussi, F., Saragosti, S., Brun-Vezinet, F., and Simon, F. (1997). Serological and virological characterization of HIV-1 group O infection in Cameroon. AIDS 11, 445-453.
31. Myers, G., MacInnes, K., and Korber, B. (1992). The emergence of simian/human immunodeficiency viruses. AIDS Res. Hum. Retroviruses 8, 373-386.
32. Nkengasong, J. N., Peeters, M., vanden Haesevelde, M., Musi, S. S., Willems, B., Ndumbe, P. M., Delaporte, E., Perret, J. L., Piot, P., and van den Groen, G. (1993). Antigenic evidence of the presence of the aberrant HIV-1ant70 virus in Cameroon and Gabon. AIDS 7, 1536-1538.
33. Peeters, M., Gueye, A., Mboup, S., Bibollet-Ruche, F., Ekaza, E., Mulanga, C., Ouedrago, R., Gandji, R., Mpele, P., Dibanga, G., Koumare, B., Saidou, M., Esu-Williams, E., Lombart, J. P., Badombena, W., Luo, N., Vanden Haesevelde, M., and Delaporte, E. (1997). Geographical distribution of HIV-1 group O viruses in Africa. AIDS 11, 493-498.
34. Peeters, M., Liegeois, F., Torimiro, N., Bourgeois, A., Mpoudi, E., Vergne, L., Saman, E., Delaporte, E., and Saragosti, S. (1999). Characterization of a highly replicative intergroup M/O human immunodeficiency virus type 1 recombinant isolated from a Cameroonian patient. J. Virol. 73, 7368-7375.
35. Pybus, O. G., Rambaut, A., and Harvey, P. H. (2000). An integrated framework for the inference of viral population history from reconstructed genealogies. Genetics 155, 1429-1437.
36. Quinones-Mateu, M. E., Albright, J. L., Mas, A., Soriano, V., and Arts, E. J. (1998). Analysis of pol gene heterogeneity, viral quasispecies, and drug resistance in individuals infected with group O strains of human immunodeficiency virus type 1. J. Virol. 72, 9002-9015.
37. Quinones-Mateu, M. E., Soriano, V., Domingo, E., and Menendez-Arias, L. (1997). Characterization of the reverse transcriptase of a human immunodeficiency virus type 1 group O isolate. Virology 236, 364-373.
38. Rambaut, A., Robertson, D. L., Pybus, O. G., Peeters, M., and Holmes, E. C. (2001). Phylogeny and the origin of HIV-1. Nature 410, 1047-1048.
39. Robertson, D. L., Anderson, J. P., Bradac, J. A., Carr, J. K., Foley, B., Funkhouser, R. K., Gao, F., Hahn, B. H., Kalish, M. L., Kuiken, C., Learn, G. H., Leitner, T., McCutchan, F., Osmanov, S., Peeters, M., Pieniazek, D., Salminen, M., Sharp, P. M., Wolinsky, S., and Korber, B. (2000). HIV-1 nomenclature proposal. Science 288, 55-56.
40. Robertson, D. L., Sharp, P. M., McCutchan, F. E., and Hahn, B. H. (1995). Recombination in HIV-1. Nature 374, 124-126.
41. Rowe, P. M. (1996). HIV-1 group O infection identified in USA. Lancet 348, 116.
42. Saitou, N., and Nei, M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
43. Schierup, M. H., and Hein, J. (2000). Consequences of recombination on traditional phylogenetic analysis. Genetics 156, 879-891.
44. Simon, F., Mauclere, P., Roques, P., Loussert-Ajaka, I., Muller-Trutwin, M. C., Saragosti, S., Georges-Courbot, M. C., Barre-Sinoussi, F., and Brun-Vezinet, F. (1998). Identification of a new human immunodeficiency virus type 1 distinct from group M and group O. Nature Med. 4, 1032-1037.
45. Songok, E. M., Libondo, D. K., Rotich, M. C., Oogo, S. A., and Tukei, P. M. (1996). Surveillance for HIV-1 subtypes O and M in Kenya. Lancet 347, 1700.
46. Sullivan, P. S., Do, A. N., Ellenberger, D., Pau, C. P., Paul, S., Robbins, K., Kalish, M., Storck, C., Schable, C. A., Wise, H., Tetteh, C., Jones, J. L., McFarland, J., Yang, C., Lal, R. B., and Ward, J. W. (2000). Human immunodeficiency virus (HIV) subtype surveillance of African-born persons at risk for group O and group N HIV infections in the United States. J. Infect. Dis. 181, 463-469.
47. Sullivan, P. S., Do, A. N., Robbins, K., Kalish, M., Subbarao, S., Pieniazek, D., Schable, C., Afaq, G., Markowitz, J., Myers, R., Joseph, J. M., and Benjamin, G. (1997). Surveillance for variant strains of HIV: Subtype G and group O HIV-1. J. Am. Med. Assoc. 278, 292.
48. Takehisa, J., Zekeng, L., Ido, E., Yamaguchi-Kabata, Y., Mboudjeka, I., Harada, Y., Miura, T., Kaptu, L., and Hayami, M. (1999). Human immunodeficiency virus type 1 intergroup (M/O) recombination in Cameroon. J. Virol. 73, 6810-6820.
49. Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994). CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
50. Vanden Haesevelde, M., Decourt, J. L., De Leys, R. J., Vanderborght, B., van der Groen, G., van Heuverswijn, H., and Saman, E. (1994). Genomic cloning and complete sequence analysis of a highly divergent African human immunodeficiency virus isolate. J. Virol. 68, 1586-1596.
51. Vidal, N., Peeters, M., Mulanga-Kabeya, C., Nzilambi, N., Robertson, D., Ilunga, W., Sema, H., Tshimanga, K., Bongo, B., and Delaporte, E. (2000). 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, 10498-10507.
52. Worobey, M. (2001). A novel approach to detecting and measuring recombination: New insights into evolution of viruses, bacteria, and mitochondria. Mol. Biol. Evol. 18, 1425-1434.
53. Yang, C., Gao, F., Funjungo, P. N., Zekeng, L., van der Groen, G., Pieniazek, D., Schable, C., and Lal, R. B. (2000). Phylogenetic analysis of protease and transmembrane region of HIV type 1 group O. AIDS Res. Hum. Retroviruses 16, 1075-1081.
54. Zekeng, L., Obiang Sima, J., Hampl, H., Ndemesogo, J. M., Ntutumu, J., Sima, V., Devare, S., Kaptue, L., and Gurtler, L. (1997). Update on HIV-1 group O infection in Equatorial Guinea, Central Africa. AIDS 11, 1410-1412.
55. Zhu, T., Korber, B. T., Nahmias, A. J., Hooper, E., Sharp, P. M., and Ho, D. D. (1998). An African HIV-1 sequence from 1959 and implications for the origin of the epidemic. Nature 391, 594-597.