Synonymous genetic polymorphisms within Brazilian human immunodefidency virus type 1 subtypes may influence mutational routes to drug resistance

Journal of Infectious Diseases

Volumn 189, Issue 7, 2004, Pages 1232-1238

  Dumans, Ana T ^a   Soares, Marcelo A ^b   Machado, Elizabeth S ^b,c   Hué, Stéphane ^d   Brindeiro, Rodrigo M ^b   Pillay, Deenan ^d   Tanuri, Amilcar ^b,c  

^a FEDERAL UNIVERSITY OF THE STATE OF RIO DE JANEIRO   (Brazil)

^b Departamento de Genetica   (Brazil)

^c FEDERAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

^d UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; PROTEINASE; PROTEINASE INHIBITOR; RNA DIRECTED DNA POLYMERASE; RNA DIRECTED DNA POLYMERASE INHIBITOR;

ARTICLE; BRAZIL; CODON; GENETIC POLYMORPHISM; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; UNINDEXED SEQUENCE; VIRUS INFECTION; VIRUS MUTATION; VIRUS RESISTANCE;

EID: 1842607676     PISSN: 00221899     EISSN: None     Source Type: Journal    
DOI: 10.1086/382483     Document Type: Article

References (31)

1. Berkhout B, Grigoriev A, Bakker M, Lukashov VV. Codon and amino acid usage in retroviral genomes is consistent with virus-specific nucleotide pressure. AIDS Res Hum Retroviruses 2002; 18:133-41.
2. Nakamura Y, Gojobori T, Ikemura T. Codon usage tabulated from the international DNA sequence databases: status for the year 2000. Nucleic Acids Res 2000; 28:292.
3. Peeters M. The genetic variability of HIV-1 and its implications. Transfus Clin Biol 2001; 8:222-5.
4. Brenner B, Turner D, Oliveira M, et al. A V106M mutation in HIV-1 clade C viruses exposed to efavirenz confers cross-resistance to non-nucleoside reverse transcriptase inhibitors. AIDS 2003; 17:F1-5.
5. Caride E, Brindeiro R, Hertogs K, et al. Drug-resistant reverse transcriptase genotyping and phenotyping of B and non-B subtypes (F and A) of human immunodeficiency virus type 1 found in Brazilian patients failing HAART. Virology 2000; 275:107-15.
6. Caride E, Hertogs K, Larder B, et al. Genotypic and phenotypic evidence of different drug-resistance mutation patterns between B and non-B subtypes isolates of human immunodeficiency virus type 1 found in Brazilian patients failing HAART. Virus Genes 2001; 23:193-202.
7. Dumans AT, Soares MA, Pieniazek D, et al. Prevalence of protease and reverse transcriptase drug resistance mutations over time in drug-naive human immunodeficiency virus type 1-positive individuals in Rio de Janeiro, Brazil. Antimicrob Agents Chemother 2002; 46:3075-9.
8. Brindeiro PA, Brindeiro RM, Mortensen C, et al. Testing genotypic and phenotypic resistance in human immunodeficiency virus type 1 isolates of clade B and other clades from children failing antiretroviral therapy. J Clin Microbiol 2002; 40:4512-9.
9. Brindeiro RM, Diaz RS, Sabino EC, et al. Brazilian Network for HIV Drug Resistance Surveillance (HIV-BResNet): a survey of chronically infected individuals. AIDS 2003; 17: 1063-9.
10. Brindeiro RM, Vanderborght B, Caride E, et al. Sequence diversity of the reverse transcriptase of human immunodeficiency virus type 1 from untreated Brazilian individuals. Antimicrob Agents Chemother 1999; 43:1674-80.
11. Cornelissen M, van den Burg R, Zorgdrager F, Lukashov V, Goudsmit J. 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. J Virol 1997; 71:6348-58.
12. Huang DD, Giesler TA, Bremer JW. Sequence characterization of the protease and partial reverse transcriptase proteins of the NED panel, an international HIV type 1 subtype reference and standards panel. AIDS Res Hum Retroviruses 2003; 19:321-8.
13. Soares MA, De Oliveira T, Brindeiro RM, et al. A specific subtype C of human immunodeficiency virus type 1 circulates in Brazil. AIDS 2003; 17:11-21.
14. Machado ES, Lambert JS, Watson DC et al. Genotypic analysis and subtypes of HIV-1 from children on dual and triple therapy in Rio de Janeiro, Brazil. J Clin Virol (in press).
15. Soares EAJM, Santos RP, Pellegrini JA, Sprinz E, Tanuri A, Soares MA. HIV drug resistance mutations in ARV-treated patients from southern Brazil [abstract 125]. Antivir Ther 2003; 8:S139.
16. Tanuri A, Vicente ACP, Otsuki K, et al. Genetic variation and susceptibilities to protease inhibitors among subtypes B and F isolates in Brazil. Antimicrob Agents Chemother 1999; 43:253-8.
17. Ramos A, Tanuri A, Schechter M, et al. Dual and recombinant infections: an integral part of the HIV-1 epidemic in Brazil. Emerg Infect Dis 1999; 5:65-74.
18. Janini LM, Pieniazek D, Peralta JM, et al. Identification of single and dual infections with distinct subtypes of human immunodeficiency virus type I by using restriction fragment length polymorphism analysis. Virus Genes 1996; 13:69-81.
19. Janini LM, Tanuri A, Schecter M, et al. Horizontal and vertical transmission of human immunodeficiency virus type 1 dual infections caused by viruses of subtypes B and C. J Infect Dis 1998; 177:227-31.
20. Potts KE, Kalish ML, Lott T, et al. Genetic heterogeneity of the V3 region of the HIV-1 envelope glycoprotein in Brazil. Brazilian Collaborative AIDS Research Group. AIDS 1993; 7:1191-7.
21. Pieniazek D, Peralta JM, Ferreira JA, et al. Identification of mixed HIV-1/HIV-2 infections in Brazil by polymerase chain reaction. AIDS 1991; 5:1293-9.
22. Vicente ACP, Otsunlk K, Silva NB, et al. The HIV epidemic in the Amazon Basin is driven by protolypic and recombinant HIV-1 subtypes B and F. J Acquir Immune Defic Syndr 2000; 23:327-31.
23. Thompson JD, Higgins DG, 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; 22:4673-80.
24. Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 1997; 13:555-6.
25. D'Aquila RT, Schapiro JM, Brun-Vézinet F, et al. Drug resistance mutations in HIV-1. Top HIV Med 2002; 10:21-5.
26. Kantor R, Machekano R, Gonzales MJ, et al. Human immunodeficiency virus reverse transcriptase and protease sequence database: an expanded data model integrating natural language text and sequence analysis programs. Nucleic Acids Res 2001; 29:296-9.
27. Miller MD, Margot NA, Hertogs K, Larder B, Miller V. Antiviral activity of tenofovir (PMPA) against nucleoside-resistant clinical HIV samples. Nucleosides Nucleotides Nudeic Acids 2001; 20:1025-8.
28. Miller V, Larder B. Mutational patterns in the HIV genome and cross-resistance following nucleoside and nucleotide analogue drug exposure. Antivir Ther 2001;6:25-44.
29. Coakley EP, Gillis JM, Hammer SM. Phenotypic and genotypic resistance patterns of HIV-1 isolates derived from individuals treated with didanosine and stavudine. AIDS 2000;14:F9-15.
30. Yahi N, Tamalet C, Tourres C, Tivoli N, Fantini J. Mutation L210W of HIV-1 reverse transcriptase in patients receiving combination therapy. Incidence, association with other mutations, and effects on the structure of mutated reverse transcriptase. J Biomed Sci 2000; 7:507-13.
31. Gonzales MJ, Wu TD, Taylor J, et al. Extended spectrum of HIV-1 reverse transcriptase mutations in patients receiving multiple nucleoside analog inhibitors. AIDS 2003; 17:791-9.