Polymorphism, recombination, and mutations in HIV type 1 gag-infecting Peruvian male sex workers

AIDS Research and Human Retroviruses

Volumn 24, Issue 11, 2008, Pages 1405-1413

  Yabar, Carlos Augusto ^a   Salvatierra, Javier ^b   Quijano, Eberth ^b  

^a INSTITUTO NACIONAL DE SALUD   (Peru)

^b Centro Especializado en Enfermedades de Transmisión Sexual Alberto Barton   (Peru)

Author keywords

[No Author keywords available]

Indexed keywords

CELL DNA; GAG PROTEIN;

ADULT; ARTICLE; CONTROLLED STUDY; DNA POLYMORPHISM; FEMALE; GENE DELETION; GENE MUTATION; GENE SEQUENCE; GENETIC POLYMORPHISM; GENETIC RECOMBINATION; GENETIC VARIABILITY; HUMAN; HUMAN CELL; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTED PATIENT; MAJOR CLINICAL STUDY; MALE; PERIPHERAL BLOOD MONONUCLEAR CELL; PERU; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROSTITUTION; PROTEIN DOMAIN; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SEQUENCE HOMOLOGY; SEX DIFFERENCE;

ADULT; DNA, VIRAL; FEMALE; GAG GENE PRODUCTS, HUMAN IMMUNODEFICIENCY VIRUS; GENOTYPE; HIV INFECTIONS; HIV-1; HUMANS; LEUKOCYTES, MONONUCLEAR; MALE; MOLECULAR SEQUENCE DATA; PERU; PHYLOGENY; POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; PROSTITUTION; RECOMBINATION, GENETIC; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY;

EID: 57049149722     PISSN: 08892229     EISSN: None     Source Type: Journal    
DOI: 10.1089/aid.2008.0130     Document Type: Article

References (46)

1. World Health Organization: AIDS epidemic update, December 2005.
2. Patrucco R: Immunological study of AIDS in Peru. Diagnostici 1985;6:122-124.
3. Oficina General de Epidemiología (OGE): Situación del VIHSIDA en el Perú. Boletín Epidemiológico Mensual. Ministerio de Salud, 2005.
4. Cabello R: La situación del VIH/SIDA en el Perú al año 2005. VIA LIBRE, 2005.
5. Yábar C, Salvatierra J, Quijano E: Características epidemiológicas del comportamiento sexual en hombres y mujeres trabajadores sexuales infectados con el virus de la inmunodeficiencia humana tipo 1 de Lima y Callao. IX Congreso Peruano de Enfermedades Infecciosas y Tropicales - II Congreso Peruano de Control de Infecciones Intrahospitalarias - I Congreso Peruano de SIDA "Dr Manuel Huaroto Sedda." Abstract 84, Lima, 2005.
6. Montano SM, Sanchez JL, Laguna-Torres A, Cuchi P, Avila MM, Weissenbacher M, et al.: Prevalences, genotypes, and risk factors for HIV transmission in South America. J Acquir Immune Defic Syndr 2005;40(1):57-64.
7. Hierholzer J, Montano S, Hoelscher M, Negrete M, Hierholzer M, Avila MM, et al.: Molecular epidemiology of HIV type 1 in Ecuador, Peru, Bolivia, Uruguay, and Argentina. AIDS Res Hum Retroviruses 2002;18(18):1339-1350.
8. Laguna-Torres VA, Olson J, Montano S, Chauca G, Carrion G, Romero A, et al.: Distribución de los subtipos del VIH-1 en nueve países de América del Sur, 1995-2002. Rev Perú Med Exp Salud Publica 2005;22(1):12-17.
9. Van der Auwera G and Heyndrick L: HIV-1 group M gag Heteroduplex Mobility Analysis (HMA) Subtyping Kit. Protocol version 3, 2000.
10. Thompson JD, Higgins DG, and Gibson TJ: CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res, 1994;22(22):4673-4680.
11. Saitou N and Nei M: The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4(4):406-425.
12. Kimura M: A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980;16:111-120.
13. Olsen GJ, Matsuda H, Hagstrom R, and Overbeek R: Fast DNAml: A tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput Appl Biosci 1994;10:41-48.
14. Felsenstein, J: Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 1981;17:368-376.
15. Martin DP, Williamson C, and Posada D: RDP2: Recombination detection and analysis from sequence alignments. Bioinformatics 2005;21(2):260-262.
16. Berkowitz R, Fisher J, and Goff SP: RNA packaging. Curr Top Microbiol Immunol 1996;214:177-218.
17. Mammano F, Ohagen A, Hoglund S, and Gottlinger HG: Role of the major homology region of human immunodeficiency virus type 1 in virion morphogenesis. J Virol 1994;68(8):4927-4936.
18. Tatt ID, Barlow KL, and Clewley JP: A gag gene heteroduplex mobility assay for subtyping HIV-1. J Virol Methods, 2000;87(1-2):41-51.
19. Heyndrickx L, Janssens W, Zekeng L, Musonda R, Anagonou S, Van der Auwera G, et al.: Simplified strategy for detection of recombinant human immunodeficiency virus type 1 group M isolates by gag/env heteroduplex mobility assay. Study Group on Heterogeneity of HIV Epidemics in African Cities. J Virol 2000;74(1):363-370.
20. Kiwelu IE, Koulinska IN, Nkya WM, Shao J, Kapiga S, and Essex M: Identification of CRF10_CD viruses among bar and hotel workers in Moshi, Northern Tanzania. AIDS Res Hum Retroviruses 2005;21(10):897-900.
21. Bhanja P, Sengupta S, Singh NY, Sarkar K, Bhattacharya SK, and Chakrabarti S: Determination of gag and env subtypes of HIV-1 detected among injecting drug users (IDUs) in Manipur, India: Evidence for intersubtype recombination. Virus Res 2005;114(1-2):149-153.
22. Wei Q and Fultz PN: Extensive diversification of human immunodeficiency virus type 1 subtype B strains during dual infection of a chimpanzee that progressed to AIDS. J Virol, 1998;72(4):3005-3017.
23. Cham F, Heyndrickx L, Janssens W, Vereecken K, De Houwer K, Coppens S, et al.: Development of a one-tube multiplex reverse transcriptase- polymerase chain reaction assay for the simultaneous amplification of HIV type 1 group M gag and env heteroduplex mobility assay fragments. AIDS Res Hum Retroviruses 2000;16(15):1503-1505.
24. Ramos A, Tanuri A, Schechter M, Rayfield MA, Hu DJ, Cabral MC, et al.: Dual and recombinant infections: An integral part of the HIV-1 epidemic in Brazil. Emerg Infect Dis 1999;5(1):65-74.
25. Flores I, Pieniazek D, Moran N, Soler A, Rodriguez N, Alegria M, et al.: HIV-1 subtype F in single and dual infections in Puerto Rico: A potential sentinel site for monitoring novel genetic HIV variants in North America. Emerg Infect Dis 1999;5(3):481-483.
26. Janini LM, Pieniazek D, Peralta JM, Schechter M, Tanuri A, Vicente AC, et al.: Identification of single and dual infections with distinct subtypes of human immunodeficiency virus type 1 by using restriction fragment length polymorphism analysis. Virus Genes 1996;13(1):69-81.
27. Grobler J, Gray CM, Rademeyer C, Seoighe C, Ramjee G, Karim SA, et al.: Incidence of HIV-1 dual infection and its association with increased viral load set point in a cohort of HIV-1 subtype C-infected female sex workers. J Infect Dis 2004;190(7):1355-1359
28. Manigart O, Courgnaud V, Sanou O, Valea D, Nagot N, Meda N, et al.: HIV-1 superinfections in a cohort of commercial sex workers in Burkina Faso as assessed by an autologous heteroduplex mobility procedure. AIDS 2004;18(12):1645-1651.
29. Fang G, Weiser B, Kuiken C, Philpott SM, Rowland-Jones S, Plummer F, et al.: Recombination following superinfection by HIV-1. AIDS 2004;18(2):153-159.
30. Bautista CT, Sanchez JL, Montano SM, Laguna-Torres VA, Lama JR, Sanchez JL, et al.: Seroprevalence of and risk factors for HIV-1 infection among South American men who have sex with men. Sex Transm Inf 2004;80;498-504
31. Manzelli H and Pecheny M: Prevención del VIH/SIDA en "Hombres que tienen sexo con hombres." In: SIDA y sexo entre hombres en América Latina: Vulnerabilidades, fortalezas, y propuestas para la acción" - Perspectivas y reflexiones desde la salud pública, las ciencias sociales y el activismo, 1st ed. (Cáceres CF, Pecheny M, Terto J, Veriano J, Eds.). UPCH/ONUSIDA, Lima, 2002, pp. 118-120.
32. CDC: Update: Impact of the expanded AIDS surveillance case definition for adolescents and adults on case reporting - United States, 1993. MMWR 1994;43:160-161,167-170.
33. Gottlieb GS, Nickle DC, Jensen MA, Wong KG, Grobler J, Li F, et al.: Dual HIV-1 infection associated with rapid disease progression. Lancet 2004;363:619-622.
34. Jost S, Bernard MC, Kaiser L, Yerly S, Hirschel B, Samri A, et al.: A patient with HIV-1 superinfection. N Engl J Med. 2002; 347(10):731-736.
35. Koelsch KK, Smith DM, Little SJ, Ignacio CC, Macaranas TR, Brown AJ, et al.: Clade B HIV-1 superinfection with wildtype virus after primary infection with drug-resistant clade B virus. AIDS 2003;17(7):F11-F16.
36. Yang OO, Daar ES, Jamieson BD, Balamurugan A, Smith DM, Pitt JA, et al.: Human immunodeficiency virus type 1 clade B superinfection: Evidence for differential immune containment of distinct clade B strains. J Virol 2005;79(2):860-868.
37. Rios M, Fernandez J, Jaramillo P, Paredes V, Sanchez JL, Laguna-Torres VA, et al.: Molecular epidemiology of HIV type 1 in Chile: Differential geographic and transmission route distribution of B and F subtypes. AIDS Res Hum Retroviruses 2005;21(10):835-840.
38. Rios M, Villanueva C, San Martin C, and Ramirez E: Identification of B and F human immunodeficiency virus subtypes in Chilean patients. Rev Med Chile 2003;131(7):711-718.
39. Csillag C: HIV-1 subtype C in Brazil. Lancet 1994;344(8933):1354.
40. Carrion G, Eyzaguirre L, Montano SM, Laguna-Torres V, Serra M, Aguayo N, et al.: Documentation of subtype C HIV type 1 strains in Argentina, Paraguay, and Uruguay. AIDS Res Hum Retroviruses 2004;20(9):1022-1025.
41. Salazar-Gonzalez JF, Bailes E, Pham KT, Salazar MG, Guffey MB, Keele BF, et al.: Deciphering human immunodeficiency virus type 1 transmission and early envelope diversification by single-genome amplification and sequencing. J Virol 2008;82(8):3952-3970.
42. Urbaneja MA, Kane BP, Johnson DG, Gorelick RJ, Henderson LE, and Casas-Finet JR: Binding properties of the human immunodeficiency virus type 1 nucleocapsid protein p7 to a model RNA: Elucidation of the structural determinants for function. J Mol Biol 1999;287(1):59-75.
43. Cen S, Huang Y, Khorchid A, Darlix JL, Wainberg MA, and Kleiman, L: The role of Pr55 (gag) in the annealing of tRNA3Lys to human immunodeficiency virus type 1 genomic RNA. J Virol 1999;73:4485-4488.
44. Feng YX, Campbell S, Harvin D, Ehresmann B, Ehresmann C, and Rein A: The human immunodeficiency virus type 1 Gag polyprotein has nucleic acid chaperone activity: Possible role in dimerization of genomic RNA and placement of tRNA on the primer binding site. J Virol 1999;73:4251-4256.
45. Dawson L and Yu XF: The role of nucleocapsid of HIV-1 in virus assembly. Virology 1998;251(1):141-157.
46. Dorfman T, Bukovsky A, Öhagen A, Höglund S, and Göttlinger HG: Functional domains of the capsid protein of human immunodeficiency virus type 1. J Virol 1994;68:8180-8187.