Analysis of HIV quasispecies suggests compartmentalization in the liver

AIDS Research and Human Retroviruses

Volumn 30, Issue 4, 2014, Pages 394-402

  Penton, Patricia K ^a   Blackard, Jason T ^a  

^a UNIVERSITY OF CINCINNATI COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GLYCOPROTEIN GP 120; NEF PROTEIN;

ARTICLE; GENE SEQUENCE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS; LIVER; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE ANALYSIS; VIRAL GENETICS;

CLUSTER ANALYSIS; ENV GENE PRODUCTS, HUMAN IMMUNODEFICIENCY VIRUS; GENETIC VARIATION; HIV; HIV INFECTIONS; HUMANS; LIVER; NEF GENE PRODUCTS, HUMAN IMMUNODEFICIENCY VIRUS; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

EID: 84898714784     PISSN: 08892229     EISSN: 19318405     Source Type: Journal    
DOI: 10.1089/aid.2013.0146     Document Type: Article

References (36)

1. Bica I, McGovern B, Dhar R, et al.: Increasing mortality due to end-stage liver disease in patients with human immunodeficiency virus infection. Clin Infect Dis 2001;32:492-497. (Pubitemid 32173638)
2. Smith C, Sabin CA, Lundgren JD, et al.: Factors associated with specific causes of death amongst HIV-positive individuals in the D:A:D Study. AIDS 2010;24(10):1537-1548.
3. Tedaldi E, Baker R, Moorman A, et al.: Influence of coinfection with hepatitis C virus on morbidity and mortality due to human immunodeficiency virus infection in the era of highly active antiretroviral therapy. Clin Infect Dis 2003;36:363-367. (Pubitemid 36169673)
4. Soriano V, Barreiro P, and Sherman K: The changing epidemiology of liver disease in HIV patients. AIDS Rev 2013; 15(1):25-31.
5. Kim AY and Chung R: Coinfection with HIV-1 and HCV-A one-two punch. Gastroenterology 2009;137(3):795-814.
6. Price JC, Seaberg EC, Badri S, Witt MD, D'Acunto K, and Thio C: HIV monoinfection is associated with increased aspartate aminotransferase-to- platelet ratio index, a surrogate marker for hepatic fibrosis. J Infect Dis 2012;205(6):1005-1013.
7. Sterling RK, Chiu S, Snider K, and Nixon D: The prevalence and risk factors for abnormal liver enzymes in HIV-positive patients without hepatitis B or C coinfections. Digest Dis Sci 2007;53(5):1375-1382.
8. Blackard JT, Welge JA, Taylor LE, et al.: HIV mono-infection is associated with FIB-4-A noninvasive index of liver fibrosis-in women. Clin Infect Dis 2011;52(5):674-680.
9. Forrester JE, Rhee MS, McGovern BH, Sterling RK, Knox TA, and Terrin N: The association of HIV viral load with indirect markers of liver injury. J Viral Hepatitis 2012;19(2):202-211.
10. Crane M, Iser D, and Lewin S: Human immunodeficiency virus infection and the liver. World J Hepatol 2012;4(3):91-98.
11. Cao YZ, Friedman-Kein AE, Huang YX, et al.: CD4-independent, productive human immunodeficiency virus type 1 infection of hepatoma cell lines in vitro. J Virol 1990;64(6):2553-2559.
12. Housset C, Lamas E, Courgnaud V, et al.: Presence of HIV-1 in human parenchymal and non-parenchymal liver cells in vivo. J Hepatol 1993;19(2):252-256.
13. Hufert FT, Schmitz J, Schreiber M, Schmitz H, Racz P, and Laer Dv: Human Kupffer cels infected with HIV-1 in vivo. J Acquir Immune Defic Syndr 1993;6(7):772-777. (Pubitemid 23183350)
14. Kong L, Cardona Maya W, Moreno-Fernandez ME, et al.: Low-level HIV infection of hepatocytes. Virol J 2012;9(1):157.
15. Tuyama AC, Hong F, Saiman Y, et al.: Human immunodeficiency virus (HIV)-1 infects human hepatic stellate cells and promotes collagen I and monocyte chemoattractant protein-1 expression: Implications for the pathogenesis of HIV/hepatitis C virus-induced liver fibrosis. Hepatology 2010;52(2):612-622.
16. Xiao P, Usami O, Suzuki Y, et al.: Characterization of a CD4-independent clinical HIV-1 that can efficiently infect human hepatocytes through chemokine (C-X-C motif) receptor 4. AIDS 2008;22(14):1749-1757.
17. Blackard JT, Ma G, Martin CM, Rouster SD, Shata MT, and Sherman K: HIV variability in the liver and evidence of possible compartmentalization. AIDS Res Hum Retroviruses 2011;27(10):1117-1126.
18. Lamers SL, Salemi M, Galligan DC, et al.: Extensive HIV-1 intra-host recombination is common in tissues with abnormal histopathology. PLoS One 2009;4(3):e5065.
19. van't Wout AB, Ran LJ, Kuiken CL, Kootstra NA, Pals ST, and Schuitemaker H: Analysis of the temporal relationship between human immunodeficiency virus type 1 quasispecies in sequential blood samples and various organs obtained at autopsy. J Virol 1998;72(1):488-496. (Pubitemid 28048863)
20. Larkin MA, Blackshields G, Brown NP, et al.: Clustal W and Clustal X version 2.0. Bioinformatics 2007;2007(23):21.
21. Felsenstein J: Confidence limits on phylogenies: An approach using the bootstrap. Evolution 1985;39:783-791.
22. Korber B and Myers G: Signature pattern analysis: A method for assessing viral sequence relatedness. AIDS Res Hum Retroviruses 1992;8(9):1549-1560.
23. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, and Kumar S: MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011;28(10): 2731-2739.
24. Collins KR, Quiñ ones-Mateu ME, Wu M, et al.: Human immunodeficiency virus type 1 (HIV-1) quasispecies at the sites of Mycobacterium tuberculosis infection contribute to systemic HIV-1 heterogeneity. J Virol 2002;76(4):1697-1706.
25. Poss M, Rodrigo AG, Gosink JJ, et al.: Evolution of envelope sequences from the genital tract and peripheral blood of women infected with clade A human immunodeficiency virus type 1. J Virol 1998;72(10):8240-8451.
26. Korber B and Gnanakaran S: The implications of patterns in HIV diversity for neutralizing antibody induction and susceptibility. Curr Opin HIV AIDS 2009;4(5):408-417.
27. Arthos J, Cicala C, Martinelli E, et al.: HIV-1 envelope protein binds to and signals through integrin alpha4beta7, the gut mucosal homing receptor for peripheral T cells. Nat Immunol 2008;9(3):301-309. (Pubitemid 351267327)
28. Zhou T, Georgiev I, Wu X, et al.: Structural basis for broad and potent neutralization of HIV-1 by antibody VRC01. Science 2010;329(5993):811-817.
29. Sanders RW, Venturi M, Schiffner L, et al.: The mannosedependent epitope for neutralizing antibody 2G12 on human immunodeficiency virus type 1 glycoprotein gp120. J Virol 2002;76(14):7293-7305.
30. HongPW,Nguyen S, Young S, Su SV, and Lee B: Identification of the optimal DC-SIGN binding site on human immunodeficiency virus type 1 gp120. J Virol 2007;81(15):8325-8336. (Pubitemid 47101517)
31. Lamers SL, Poon AF, and McGrath M: HIV-1 nef protein structures associated with brain infection and dementia pathogenesis. PLoS One 2011;6(2):e16659.
32. Nguyen DG and Hildreth J: Involvement of macrophage mannose receptor in the binding and transmission of HIV by macrophages. Eur J Immunol 2003;33(2):483-493. (Pubitemid 36267614)
33. Geijtenbeek T, Kwon DS, van Vliet SJ, et al.: DC-SIGN, a dendritic cell-specific HIV-1 binding protein that enhances trans-infection of T cells. Cell 2000;100(3):587-597.
34. Popik W and Pitha P: Exploitation of cellular signaling by HIV-1: Unwelcome guests with master keys that signal their entry. Virology 2000;276(1):1-6.
35. Blackard JT and Sherman K: HCV/HIV co-infection: Time to re-evaluate the role of HIV in the liver J Viral Hepatitis 2008;15(5):323-330. (Pubitemid 351473633)
36. Bansal M and Blackard J: Effects of HIV on liver cell populations. Springer Science + Business Media, New York, 2012.