Genetic differences between human immunodeficiency virus type 1 subpopulations in faeces and serum

References

1. Albert J., Abrahamsson B., Nagy K., Aurelius E., Gaines H., Nyström G., Fenyö E.-M. 1990; Rapid development of isolate-specific neutralizing antibodies after primary HIV-1 infection and consequent emergence of virus variants which resist neutralization by autologous sera. AIDS 4:107–112
   [Google Scholar]
2. Barnett S. W., Barboza A., Wilcox C. M., Forsmark C. E., Levy J. A. 1991; Characterization of human immunodeficiency virus type 1 strains recovered from the bowel of infected individuals. Virology 182:802–809
   [Google Scholar]
3. 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]
4. de Jong J. J., Goudsmit J., Keulen W., Klaver B., Krone W., Tersmette M., de Ronde A. 1992; Human immunodeficiency virus type 1 clones chimeric for the envelope V3 domain differ in syncytium formation and replication capacity. Journal of Virology 66:757–765
   [Google Scholar]
5. Donaldson Y. K., Bell J. E., Holmes E. C., Hughes E. S., Brown H. K., Simmonds P. 1994; In vivo distribution and cytopathology of variants of human immunodeficiency virus type 1 showing restricted sequence variability in the V3 loop. Journal of Virology 68:5991–6005
   [Google Scholar]
6. Epstein L. G., Kuiken C., Blumberg B. M., Hartman S., Sharer L. R., Clement M., Goudsmit J. 1991; HIV-1 V3 domain variation in brain and spleen of children with AIDS: tissue-specific evolution within host-determined quasispecies. Virology 180:583–590
   [Google Scholar]
7. Felsenstein J. 1993; PHYLIP Manual version 3.5.
   [Google Scholar]
8. Fouchier R. A. M., Groenink M., Kootstra N. A., Tersmette M., Huisman H. G., Miedema F., Schuitemaker H. 1992; Phenotype associated sequence variation in the third variable domain of the human immunodeficiency virus type 1 gp120 molecule. Journal of Virology 66:3183–3187
   [Google Scholar]
9. Heise C., Dandekar S., Kumar P., Duplantier R., Donovan R. M., Halsted C. H. 1991; Human immunodeficiency virus infection of enterocytes and mononuclear cells in human jejunal mucosa. Gastroenterology 100:1521–1527
   [Google Scholar]
10. Heise C., Miller C. J., Lackner A., Dandekar S. 1994; Primary acute simian immunodeficiency virus infection of intestinal lymphoid tissue is associated with gastrointestinal dysfunction. Journal of Infectious Diseases 169:1116–1120
    [Google Scholar]
11. Hwang S. S., Boyle T. J., Lyerly H. K., Cullen B. R. 1991; Identification of the envelope V3 loop as the primary determinant of cell tropism in HIV-1. Science 253:71–74
    [Google Scholar]
12. Janoff E. N., Jackson S., Wahl S. M., Thomas K., Peterman J. H., Smith P. D. 1994; Intestinal mucosal immunoglobulins during human immunodeficiency virus type 1 infection. Journal of Infectious Diseases 170:299–307
    [Google Scholar]
13. Jarry A., Cortez A., René E., Muzeau F., Brousse N. 1990; Infected cells and immune cells in the gastrointestinal tract of AIDS patients. An immunohistochemical study of 127 cases. Histopathology 16:133–140
    [Google Scholar]
14. Javaherian K., Langlois A. J., Larosa G. J., Profy A. T., Bolognesi D. P., Herlihy W. C., Putney S. D., Matthews T. J. 1990; Broadly neutralizing antibodies elicited by the hypervariable neutralizing determinant of HIV-1. Science 250:1590–1593
    [Google Scholar]
15. 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
    [Google Scholar]
16. Korber B. T. M., Kunstman K. J., Patterson B. K., Furtado M., McEvilly M. M., Levy R., Wolinsky S. M. 1994; Genetic differences between blood- and brain-derived viral sequences from human immunodeficiency virus type 1-infected patients : evidence of conserved elements in the V3 region of the envelope protein of brain-derived sequences. Journal of Virology 68:7467–7481
    [Google Scholar]
17. Kotler D. P., Scholes J. V., Tierney A. R. 1987; Intestinal plasma cell alterations in the acquired immunodeficiency syndrome. Digestive Diseases and Sciences 32:129–138
    [Google Scholar]
18. Kotler D. P., Reka S., Borcich A., Cronin W. J. 1991; Detection, localization and quantitation of HIV-associated antigens in intestinal biopsies from patients with HIV. American Journal of Pathology 139:823–830
    [Google Scholar]
19. Kozlowski P. A., Chen D., Eldridge J. H., Jackson S. 1994; Contrasting IgA and IgG neutralization capacities and responses to HIV type 1 gp120 V3 loop in HIV-infected individuals. AIDS Research and Human Retroviruses 10:813–822
    [Google Scholar]
20. Kuiken C. L., Goudsmit J., Weiller G. F., Armstrong J. S., Hartman S., Portegies P., Dekker J., Cornelissen M. 1995; Differences in human immunodeficiency virus type 1 V3 sequences from patients with and without AIDS dementia complex. Journal of General Virology 76:175–180
    [Google Scholar]
21. Kuiken C. L., Cornelissen M. T. E., Zorgdrager F., Hartman S., Gibbs A. J., Goudsmit J. 1996; Consistent risk group associated differences in human immunodeficiency virus type 1 vpr, vpu and V3 sequences despite independent evolution. Journal of General Virology 77:783–792
    [Google Scholar]
22. Kumar S., Tamura K., Wei M. 1993; Molecular evolutionary genetics analysis (MEGA). version 1.0 Institute of Molecular Evolutionary Genetics, Pennsylvania State University:
    [Google Scholar]
23. Levy J. A. 1993; Pathogenesis of human immunodeficiency virus infection. Microbiological Reviews 57:183–289
    [Google Scholar]
24. Lukashov V. V., Kuiken C. L., Goudsmit J. 1995; Intrahost human immunodeficiency virus type 1 evolution is related to length of the immunocompetent period. Journal of Virology 69:6911–6916
    [Google Scholar]
25. Moss A. R., Osmond D., Bacchetti P., Chermann J.-C., Barre-Sinoussi F., Carlson J. 1987; Risk factors for AIDS and HIV seropositivity in homosexual men. American Journal of Epidemiology 125:1035–1047
    [Google Scholar]
26. Myers G., Korber B., Foley B., Jeang K.-T., Mellors J. W., Wainhobson S. 1996 Human Retroviruses and AIDS Los Alamos, N. Mex: Los Alamos National Laboratory;
    [Google Scholar]
27. Nara P. L., Smit L., Dunlop N., Hatch W., Merges M., Waters D., Kelliher J., Gallo R. C., Fischinger P. J., Goudsmit J. 1990; Emergence of viruses resistant to neutralization by V3-specific antibodies in experimental human immunodeficiency virus type 1 IIIB infection of chimpanzees. Journal of Virology 64:3779–3791
    [Google Scholar]
28. Nelson J. A., Reynolds-Kohler C., Margaretten W., Wiley C. A., Reese C. E., Levy J. A. 1988; Human immunodeficiency virus detected in bowel epithelium from patients with gastrointestinal symptoms. Lancet i:259–262
    [Google Scholar]
29. O’Brien W. A., Koyanagi Y., Namazie A., Zhoa J., Diagne A., Idler K., Zack J. A., Chen I. S. Y. 1990; HIV-1 tropism for mononuclear phagocytes can be determined by regions of gp120 outside the CD4-binding domain. Nature 348:69–73
    [Google Scholar]
30. Overbaugh J., Anderson R. J., Ndinya-Acola J. O., Kreiss J. K. 1996; Distinct but related human immunodeficiency virus type 1 variant populations in genital secretions and blood. AIDS Research and Human Retroviruses 12:107–115
    [Google Scholar]
31. Riecken E. O., Zeitz M., Ullrich R. 1990; Non-opportunistic causes of diarrhoea in HIV infection. In Gastroenterological Aspects of AIDS Baillièrés Clinical Gastroenterology pp. 385–403 Gazzard B. G. Edited by London: Baillière Tindall;
    [Google Scholar]
32. Saag M. S., Hahn B. H., Gibbons J., Li Y., Parks E. S., Parks W. P., Shaw G. M. 1988; Extensive variation of human immunodeficiency virus type 1 in vivo. Nature 334:440–444
    [Google Scholar]
33. Schneider T., Jahn H.-U., Schmidt W., Riecken E.-O., Zeitz M., Ullrich R. Berlin Diarrhoea/Wasting Syndrome Study Group 1995; Loss of CD4 T lymphocytes in patients infected with human immunodeficiency virus type 1 is more pronounced in the duodenal mucosa than in the peripheral blood. Gut 37:524–529
    [Google Scholar]
34. Shioda T., Levy J. A., Cheng-Mayer C. 1991; Macrophage and T cell-line tropisms of HIV-1 are determined by specific regions of the envelope gp120 gene. Nature 349:167–169
    [Google Scholar]
35. Snijders F., Meenan J., van den Blink B., van Deventer S. J. H., ten Kate F. J. W. 1996; Duodenal intraepithelial and lamina propria T-lymphocytes in human immunodeficiency virus-infected patients with and without diarrhoea. Scandinavian Journal of Gastroenterology 31:1176–1181
    [Google Scholar]
36. Ullrich R., Zeitz M., Heise W., I’Age M., Höffken G., Riecken E. O. 1989; Small intestinal structure and function in patients infected with human immunodeficiency virus (HIV): evidence for HIV-induced enteropathy. Annals of Internal Medicine 111:15–21
    [Google Scholar]
37. van der Hoek L., Boom R., Goudsmit J., Snijders F., Sol C. J. A. 1995; Isolation of human immunodefiency virus type 1 (HIV-1) RNA from feces by a simple method and difference between HIV-1 subpopulations in feces and serum. Journal of Clinical Microbiology 33:581–588
    [Google Scholar]
38. van der Hoek L., Sol C. J. A., Snijders F., Bartelsman J. F. W., Boom R., Goudsmit J. 1996; Human immunodeficiency virus type 1 RNA populations in faeces with higher homology to intestinal populations than to blood populations. Journal of General Virology 77:2415–2425
    [Google Scholar]
39. van Griensven G. J. P., Tielman R. A. P., Goudsmit J., van der Noordaa J., de Wolf F., de Vroome E. M. M., Coutinho R. A. 1987; Risk factors and prevalence of HIV antibodies in homosexual men in The Netherlands. American Journal of Epidemiology 125:1048–1057
    [Google Scholar]
40. Zhu T., Wang N., Carr A., Nam D. S., Moor-Jankowski R., Cooper D. A., Ho D. D. 1996; Genetic characterization of human immunodeficiency virus in blood and genital secretions : evidence for viral compartmentalization and selection during sexual transmission. Journal of Virology 70:3098–3107
    [Google Scholar]
41. Zwart G., Back N. K. T., Ramautarsing C., Valk M., van der Hoek L., Goudsmit J. 1994; Frequent and early HIV-1MN neutralizing capacity in sera from Dutch HIV-1 seroconverters is related to antibody reactivity to peptides from the gp120 V3 domain. AIDS Research and Human Retroviruses 10:245–251
    [Google Scholar]