1887

Abstract

To identify new subtype G human immunodeficiency virus type 1 (HIV-1) strains and AG recombinant forms, we collected 28 serum samples from immigrants to the Netherlands from 12 countries throughout Africa. Based on the sequences 22 isolates were identified as subtype A or G. Phylogenetic analysis of discontinuous regions ofthe (726 nt), (1176 nt) and (276 nt) genes revealed 13 AG recombinants with the mosaic structure A/G/A, three with A/G/G and one other with A /G/G , in addition to ‘pure’ subtypes A/A/A (=1) and G/G/G (=4). To analyse the crossover points in more detail, a new RT–PCR was developed resulting in a large contiguous sequence of 2600 nt from the region to half the region. All the 13 A/G/A recombinants appeared to belong to the circulating recombinant form (CRF) AG (IbNG). The three A/G /G recombinants differed from the CRF AG (IbNG) subtype, suggesting the identification of a new CRF subtype. The recovery of AG recombinants from African countries a thousand miles apart indicates the active spread of new recombinants.

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2000-02-01
2024-03-28
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References

  1. Abimiku, A. G., Stern, T. L., Zwandor, A., Markham, P. D. & Calef, C. (1994). Subgroup G HIV type 1 isolates from Nigeria. AIDS Research and Human Retroviruses 10, 1581-1583.[CrossRef] [Google Scholar]
  2. Alaeus, A., Leitner, T., Lidman, K. & Albert, J. (1997). Most HIV-1 genetic subtypes have entered Sweden. AIDS 11, 199-202.[CrossRef] [Google Scholar]
  3. Alizon, M., Wain-Hobson, S., Montagnier, L. & Sonigo, P. (1986). Genetic variability of the AIDS virus: nucleotide sequence analysis of two isolates from African patients. Cell 46, 63-74.[CrossRef] [Google Scholar]
  4. Benn, S., Rutledge, R., Folks, T., Gold, J., Baker, L., McCormick, J., Feorino, P., Piot, P., Quinn, T. & Martin, M. (1985). Genomic heterogeneity of AIDS retroviral isolates from North America and Zaire. Science 230, 949-951.[CrossRef] [Google Scholar]
  5. Boom, R., Sol, C. J. A., Salimans, M. M. M., Jansen, C. L., Wertheim-van Dillen, P. M. E. & van der Noordaa, J. (1990). Rapid and simple method for purification of nucleic acids. Journal of Clinical Microbiology 28, 495-503. [Google Scholar]
  6. Carr, J. K., Salminen, M. O., Koch, C., Gotte, D., Artenstein, A. W., Hegerich, P. A., St Louis, D., Burke, D. & McCutchan, F. E. (1996). Full-length sequences and mosaic structure of human immunodeficiency type 1 isolate from Thailand. Journal of Virology 70, 5935-5943. [Google Scholar]
  7. Carr, J. K., Salminen, M. O., Albert, J., Sanders-Buell, E., Gotte, D., Birx, D. L. & McCutchan, F. E. (1998). Full genome sequences of human immunodeficiency virus type 1 subtypes G and A/G intersubtype recombinants. Virology 247, 22-31.[CrossRef] [Google Scholar]
  8. Choi, D. J., Dube, S., Spicer, T. P., Slade, H. B., Jensen, F. C. & Poiesz, B. J. (1997). HIV type 1 Z321, the strain used to make a therapeutic HIV type 1 immunogen, is intersubtype recombinant. AIDS Research and Human Retroviruses 13, 357-361.[CrossRef] [Google Scholar]
  9. Clewly, J. P., Arnold, C., Barlow, K. L., Grant, P. R. & Parry, J. V. (1996). Diverse HIV-1 genetic subtypes in UK. Lancet 347, 1487.[CrossRef] [Google Scholar]
  10. Coffin, J. M. (1995). HIV population dynamics in vivo: implications for genetic variation, pathogenesis and therapy. Science 267, 483-489.[CrossRef] [Google Scholar]
  11. Cornelissen, M., Mulder-Kampinga, G., Veenstra, J., Zorgdrager, F., Kuiken, C., Hartman, S., Dekker, J., van der Hoek, L., Sol, C., Coutinho, R. & Goudsmit, J. (1995). Syncytium-inducing (SI) phenotype suppression at seroconversion after intramuscular inoculation of a non-syncytium-inducing/SI phenotypically mixed human immunodeficiency virus population. Journal of Virology 69, 1810-1818. [Google Scholar]
  12. Cornelissen, M., Kampinga, G., Zorgdrager, F., Goudsmit, J. & UNAIDS Network for HIV Isolation and Characterization (1996). Human immunodeficiency virus type 1 subtypes defined by env show high frequency of recombinant gag genes. Journal of Virology 70, 8209–8212. [Google Scholar]
  13. Cornelissen, M., van den Burg, R., Zorgdrager, F., Lukashov, V. & Goudsmit, J. (1997). Pol gene diversity of five human immunodeficiency virus type 1 subtypes: evidence for naturally occurring mutations that contribute to drug resistance, limited recombination patterns and common ancestry for subtypes B and D. Journal of Virology 71, 6348-6358. [Google Scholar]
  14. Dube, D. K., Dube, S., Erensoy, S., Jones, P., Bryz-Gornia, V., Spicer, T., Love, J., Saksena, N., Lechat, M. F., Shrager, D. I., Dosik, H., Glaser, J., Levis, W., Blattner, W., Montagna, R., Blumberg, B. S. & Poiesz, B. J. (1994). Serological and nucleic acid analyses for HIV and HTLV infection on archival human plasma samples from Zaire. Virology 202, 379-389.[CrossRef] [Google Scholar]
  15. Franzen, L., Buve, A., Nkengasong, J. N., Lage, M. & van der Groen, G. (1996). Longstanding presence in Belgians of multiple non-B HIV 1 subtypes. Lancet 347, 1403.[CrossRef] [Google Scholar]
  16. Gao, F., Robertson, D. L., Morrison, S. G., Hui, H., Craig, S., Decker, J., Fultz, P. N., Girard, M., Shaw, G. M., Hahn, B. H. & Sharp, P. M. (1996). The heterosexual human immunodeficiency virus type 1 epidemic in Thailand is caused by an intersubtype (A/E) recombinant of African origin. Journal of Virology 70, 7013-7029. [Google Scholar]
  17. Gao, F., Robertson, D. L., Carruthers, C. D., Morrison, S. G., Jian, B., Jhen, Y., Barré-Sinoussi, F., Girard, M., Srinivasan, A., Abimiku, A. G., Shaw, G. M., Sharp, P. M. & Hahn, B. H. (1998). A comprehensive panel of near-full-length clones and reference sequences for non-subtype B isolates of human immunodeficiency virus type 1. Journal of Virology 72, 5680-5698. [Google Scholar]
  18. Getchell, J. P., Hicks, D. R., Svinivasan, I., Heath, J. L., York, D. A., Malonga, M., Forthal, D. N., Mann, J. M. & McCormick, J. B. (1987). Human immunodeficiency virus isolated from a serum sample collected in 1976 in Central Africa. Journal of Infectious Diseases 156, 833-837.[CrossRef] [Google Scholar]
  19. Hillis, D. M. & Bull, J. J. (1993). An empirical test for bootscanning as a method for assessing confidence in phylogenetic analysis. Systematic Biology 42, 182-192.[CrossRef] [Google Scholar]
  20. Howard, T. M. & Rasheed, S. (1996). Genomic structure and nucleotide sequence analysis of a new HIV type A strain from Nigeria. AIDS Research and Human Retroviruses 12, 1413-1425.[CrossRef] [Google Scholar]
  21. Janssens, W. L., Heyndrickx, L., Fransen, K., Motte, J., Peeters, M., Nkengasong, J. N., Ndumbe, P. M., Delaporte, E., Perret, J.-L., Atende, C., Piot, P. & van der Groen, G. (1994). Genetic and phylogenetic analysis of env subtypes G and H in Central Africa. AIDS Research and Human Retroviruses 10, 877-879. [Google Scholar]
  22. Janssens, W. L., Buvé, A. & Nkengasong, J. N. (1997). The puzzle of HIV-1 subtypes in Africa. AIDS 11, 705-712.[CrossRef] [Google Scholar]
  23. Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitution through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16, 111-120.[CrossRef] [Google Scholar]
  24. Korber, B. T. M., Osmanov, S., Esparza, J., Myers, G. & WHO Network for HIV Isolation and Characterization (1994). The World Health Organization global programme on AIDS proposal for standardization of HIV sequence nomenclature. AIDS Research and Human Retroviruses 11, 1355–1358. [Google Scholar]
  25. Korber, B., Kuiken, C., Foley, B., Hahn, B., McCutchan, F., Mellors, J. & Sodroski, J. (1998).Human Retroviruses and AIDS 1998. A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences. Los Alamos, NM: Theoretical Biology and Biophysics, Los Alamos National Laboratory.
  26. Kumar, S., Tamura, K. & Wei, M. (1993). MEGA: molecular evolutionary genetics analysis, version 1.0. PA 16802, Pennsylvania.
  27. Leitner, T., Escanilla, D., Marquina, S., Wahlberg, J., Brostrom, C., Hansson, H. B., Uhlen, M. & Albert, J. (1995). Biological and molecular characterization of subtype D, G, and A/D recombinant HIV-1 transmissions in Sweden. Virology 209, 136-146.[CrossRef] [Google Scholar]
  28. Louwagie, J., McCutchan, F. E., Peeters, M., Brennan, T. P., Sanders, B. E., Eddy, G. A., van der Groen, G., Fransen, K., Gershy-Damet, G.-M., Deleys, R. & Burke, D. S. (1993). Phylogenetic analysis of gag genes from 70 international HIV-1 isolates provides evidence for multiple genotypes. AIDS 7, 769-780.[CrossRef] [Google Scholar]
  29. Lukashov, V. V. & Goudsmit, J. (1997). Evolution of the human immunodeficiency virus type 1 subtype-specific V3 domain is confined to a sequence space with fixed distance to the subtype consensus. Journal of Virology 71, 6332-6338. [Google Scholar]
  30. Mansky, L. M. & Temin, H. M. (1996). Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase. Journal of Virology 69, 5087-5094. [Google Scholar]
  31. Olaleye, D. O., Sheng, Z., Howard, T. M. & Rasheed, S. (1996). Isolation and characterization of a new subtype A variant of human immunodeficiency virus type 1 from Nigeria. Tropical Medicine and International Health 1, 97-106.[CrossRef] [Google Scholar]
  32. Op de Coul, E. L. M., Lukashov, V. V., van Doornum, G. J. J., Goudsmit, J. & Coutinho, R. A. (1998). Multiple HIV-1 subtypes present among heterosexuals in Amsterdam 1988–1996: no evidence for spread of non-B subtypes. AIDS 12, 1253-1255.[CrossRef] [Google Scholar]
  33. Ou, C. Y., Takebe, Y., Weniger, B. G., Luo, C. C., Kalish, M. L., Auwanit, W., Yamazaki, S., Gayle, H. D., Young, N. L. & Schochetman, G. (1993). Independent introduction of two major HIV-1 genotypes into distinct high-risk populations in Thailand. Lancet 341, 1171-1174.[CrossRef] [Google Scholar]
  34. Ray, S. C. (1999). Simplot for Windows. (http://www.med.jhu.edu/deptmed/scray/download/simplot).
  35. Robertson, D. L., Sharp, P. M., McCutchan, F. E. & Hahn, B. H. (1995). Recombination in HIV-1. Nature 374, 124-126. [Google Scholar]
  36. Schuurman, R., Nijhuis, M., van Leeuwen, R., Schipper, P., de Jong, D., Collis, P., Danner, S. A., Mulder, J., Loveday, C., Christopherson, C., Kwok, S., Sninsky, J. & Boucher, C. A. B. (1995). Rapid changes in human immunodeficiency virus 1 RNA load and appearance of drug resistance mutations in individuals treated with lamivudine. Journal of Infectious Diseases 171, 1411-1419.[CrossRef] [Google Scholar]
  37. Shaw, G. M., Hahn, B. H., Arya, S. K., Groopman, J. E., Gallo, R. C. & Wong-Staal, F. (1984). Molecular characterization of human T-cell leukemia (lymphotropic) virus type III in the acquired immune deficiency syndrome. Science 226, 1165-1171.[CrossRef] [Google Scholar]
  38. Starcich, B. R., Hahn, B. H., Shaw, G. M., McNeely, P. D., Modrow, S., Wolf, H., Parks, E. S., Parks, W. P., Josephs, S. F., Gallo, R. C. & Wong-Staal, F. (1986). Identification and characterization of conserved and variable regions in the envelope gene of HTLVIII/LAV, the retrovirus of AIDS. Cell 45, 637-648.[CrossRef] [Google Scholar]
  39. Wei, X., Ghosh, S. K., Taylor, M. E., Johnson, V. A., Emini, E. A., Deutsch, P., Lifson, J. D., Bonhoeffer, S., Nowak, M. A., Hahn, B. H., Saag, M. S. & Shaw, G. M. (1995). Viral dynamics in human immunodeficiency virus type 1 infection. Nature 373, 117-122.[CrossRef] [Google Scholar]
  40. Wong-Staal, F., Shaw, G. M., Hahn, B. H., Salahuddin, S. Z., Popovic, M., Markham, P., Redfield, R. & Gallo, R. C. (1985). Genomic diversity of human T-lymphotropic virus type III (HTLV-III). Science 229, 759-762.[CrossRef] [Google Scholar]
  41. Zhu, T., Korber, B. T., Nahmias, A. J., Hooper, E., Sharp, P. M. & Ho, D. D. (1998). An African HIV-1 sequence from 1959 and implications for the origin of the epidemic. Nature 391, 594-597.[CrossRef] [Google Scholar]
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