Origin and epidemiological history of HIV-1 CRF14_BG

PLoS ONE

Volumn 6, Issue 9, 2011, Pages

  Bártolo, Inês ^a,b   Abecasis, Ana B ^c   Borrego, Pedro ^a,b   Barroso, Helena ^a,b   McCutchan, Francine ^d   Gomes, Perpétua ^b,c,e   Camacho, Ricardo ^c,e   Taveira, Nuno ^a,b  

^a RESEARCH INSTITUTE FOR MEDICINES IMED ULISBOA   (Portugal)

^b INSTITUTO SUPERIOR DE CIÊNCIAS DA SAÚDE EGAS MONIZ   (Portugal)

^c INSTITUTO DE HIGIENE E MEDICINA TROPICAL   (Portugal)

^d BILL AND MELINDA GATES FOUNDATION   (United States)

^e HOSPITAL EGAS MONIZ   (Portugal)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; CHEMOKINE RECEPTOR CXCR4;

ARTICLE; CHEMICAL STRUCTURE; CLUSTER ANALYSIS; CONTROLLED STUDY; ENVELOPE GENE; EPIDEMIOLOGICAL DATA; ETHNIC GROUP; FEMALE; GENE SEQUENCE; GENETIC VARIABILITY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; HUMAN IMMUNODEFICIENCY VIRUS INFECTED PATIENT; MAJOR CLINICAL STUDY; MALE; MOLECULAR CLOCK; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PORTUGAL; PORTUGUESE; PREVALENCE; PROMOTER REGION; SPANISH; VIRAL TROPISM; VIRUS CLASSIFICATION; VIRUS GENOME; VIRUS ISOLATION; VIRUS STRAIN;

ANTIBODIES, NEUTRALIZING; DNA; FEMALE; GENE PRODUCTS, ENV; GENES, ENV; GENOME; GENOMICS; HIV-1; HUMANS; MALE; MOLECULAR SEQUENCE DATA; PHYLOGENY; PORTUGAL; RECEPTORS, CXCR4; SEQUENCE ANALYSIS, DNA;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 80053252119     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0024130     Document Type: Article

References (49)

1. UNAIDS (2010) UNAIDS report on the global AIDS epidemic 2010. Geneve. http://www.unaids.org/GlobalReport/Global_report.htm. Geneve: UNAIDS.
2. Instituto Nacional de Saúde Dr. Ricardo Jorge, Departamento de Doenças Infecciosas, Unidade de Referência e Vigilância Epidemiológica, Núcleo de Vigilância Laboratorial de Doenças Infecciosas (2009) Infecção VIH/SIDA, A situação em Portugal a 31 de Dezembro de 2008 Lisbon.
3. Palma AC, Araujo F, Duque V, Borges F, Paixao MT, et al. (2007) Molecular epidemiology and prevalence of drug resistance-associated mutations in newly diagnosed HIV-1 patients in Portugal. Infect Genet Evol 7: 391-398.
4. Esteves A, Parreira R, Venenno T, Franco M, Piedade J, et al. (2002) Molecular epidemiology of HIV type 1 infection in Portugal: high prevalence of non-B subtypes. AIDS Res Hum Retroviruses 18: 313-325.
5. Duque V, Holguin A, Silvestre M, Gonzalez-Lahoz J, Soriano V, (2003) Human immunodeficiency virus type 1 recombinant B/G subtypes circulating in Coimbra, Portugal. Clin Microbiol Infect 9: 422-425.
6. Esteves A, Parreira R, Piedade J, Venenno T, Franco M, et al. (2003) Spreading of HIV-1 subtype G and envB/gagG recombinant strains among injecting drug users in Lisbon, Portugal. AIDS Res Hum Retroviruses 19: 511-517.
7. Araujo FM, Henriques IS, Monteiro FP, Meireles ER, Cunha-Ribeiro LM, (2004) Detection of HIV-1 subtype G using Cobas Ampliscreen test. J Clin Virol 30: 205-206.
8. Antunes R, Figueiredo S, Bartolo I, Pinheiro M, Rosado L, et al. (2003) Evaluation of the clinical sensitivities of three viral load assays with plasma samples from a pediatric population predominantly infected with human immunodeficiency virus type 1 subtype G and BG recombinant forms. J Clin Microbiol 41: 3361-3367.
9. Abecasis AB, Martins A, Costa I, Carvalho AP, Diogo I, et al. (2011) Molecular Epidemiological Analysis of Paired pol/env Sequences from Portuguese HIV Type 1 Patients. AIDS Res Hum Retroviruses 27: 803-805.
10. Delgado E, Thomson MM, Villahermosa ML, Sierra M, Ocampo A, et al. (2002) Identification of a newly characterized HIV-1 BG intersubtype circulating recombinant form in Galicia, Spain, which exhibits a pseudotype-like virion structure. J Acquir Immune Defic Syndr 29: 536-543.
11. Harris B, von Truchsess I, Schatzl HM, Devare SG, Hackett J Jr, (2005) Genomic characterization of a novel HIV type 1 B/G intersubtype recombinant strain from an injecting drug user in Germany. AIDS Res Hum Retroviruses 21: 654-660.
12. Adojaan M, Kivisild T, Mannik A, Krispin T, Ustina V, et al. (2005) Predominance of a rare type of HIV-1 in Estonia. J Acquir Immune Defic Syndr 39: 598-605.
13. Menzo S, Castagna A, Monachetti A, Hasson H, Danise A, et al. (2004) Genotype and phenotype patterns of human immunodeficiency virus type 1 resistance to enfuvirtide during long-term treatment. Antimicrob Agents Chemother 48: 3253-3259.
14. Xu L, Pozniak A, Wildfire A, Stanfield-Oakley SA, Mosier SM, et al. (2005) Emergence and evolution of enfuvirtide resistance following long-term therapy involves heptad repeat 2 mutations within gp41. Antimicrob Agents Chemother 49: 1113-1119.
15. Parreira R, Padua E, Piedade J, Venenno T, Paixao MT, et al. (2005) Genetic analysis of human immunodeficiency virus type 1 nef in Portugal: subtyping, identification of mosaic genes, and amino acid sequence variability. J Med Virol 77: 8-16.
16. de Mendoza C, Rodriguez C, Colomina J, Tuset C, Garcia F, et al. (2005) Resistance to nonnucleoside reverse-transcriptase inhibitors and prevalence of HIV type 1 non-B subtypes are increasing among persons with recent infection in Spain. Clin Infect Dis 41: 1350-1354.
17. Holguin A, Alvarez A, Soriano V, (2005) Heterogeneous nature of HIV-1 recombinants spreading in Spain. J Med Virol 75: 374-380.
18. Holguin A, de Mulder M, Yebra G, Lopez M, Soriano V, (2008) Increase of non-B subtypes and recombinants among newly diagnosed HIV-1 native Spaniards and immigrants in Spain. Curr HIV Res 6: 327-334.
19. Lospitao E, Alvarez A, Soriano V, Holguin A, (2005) HIV-1 subtypes in Spain: a retrospective analysis from 1995 to 2003. HIV Med 6: 313-320.
20. Perez-Alvarez L, Delgado E, Villahermosa ML, Cuevas MT, Garcia V, et al. (2002) Biological characteristics of newly described HIV-1 BG recombinants in Spanish individuals. AIDS 16: 669-672.
21. Perez-Alvarez L, Munoz M, Delgado E, Miralles C, Ocampo A, et al. (2006) Isolation and biological characterization of HIV-1 BG intersubtype recombinants and other genetic forms circulating in Galicia, Spain. J Med Virol 78: 1520-1528.
22. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG, (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876-4882.
23. Cuevas MT, Fernandez-Garcia A, Pinilla M, Garcia-Alvarez V, Thomson M, et al. (2010) Short communication: Biological and genetic characterization of HIV type 1 subtype B and nonsubtype B transmitted viruses: usefulness for vaccine candidate assessment. AIDS Res Hum Retroviruses 26: 1019-1025.
24. Bartolo I, Camacho R, Barroso H, Bezerra V, Taveira N, (2009) Rapid clinical progression to AIDS and death in a persistently seronegative HIV-1 infected heterosexual young man. AIDS 23: 2359-2362.
25. De Jong JJ, De Ronde A, Keulen W, Tersmette M, Goudsmit J, (1992) Minimal requirements for the human immunodeficiency virus type 1 V3 domain to support the syncytium-inducing phenotype: analysis by single amino acid substitution. J Virol 66: 6777-6780.
26. Resch W, Hoffman N, Swanstrom R, (2001) Improved success of phenotype prediction of the human immunodeficiency virus type 1 from envelope variable loop 3 sequence using neural networks. Virology 288: 51-62.
27. Perez L, Thomson MM, Bleda MJ, Aragones C, Gonzalez Z, et al. (2006) HIV Type 1 molecular epidemiology in cuba: high genetic diversity, frequent mosaicism, and recent expansion of BG intersubtype recombinant forms. AIDS Res Hum Retroviruses 22: 724-733.
28. Daar ES, Kesler KL, Petropoulos CJ, Huang W, Bates M, et al. (2007) Baseline HIV type 1 coreceptor tropism predicts disease progression. Clin Infect Dis 45: 643-649.
29. Raymond S, Delobel P, Mavigner M, Cazabat M, Encinas S, et al. (2010) CXCR4-using viruses in plasma and peripheral blood mononuclear cells during primary HIV-1 infection and impact on disease progression. Aids 24: 2305-2312.
30. Goetz MB, Leduc R, Kostman JR, Labriola AM, Lie Y, et al. (2009) Relationship between HIV coreceptor tropism and disease progression in persons with untreated chronic HIV infection. J Acquir Immune Defic Syndr 50: 259-266.
31. Kuritzkes DR, (2008) HIV-1 subtype as a determinant of disease progression. J Infect Dis 197: 638-639.
32. Sacktor N, Nakasujja N, Skolasky RL, Rezapour M, Robertson K, et al. (2009) HIV subtype D is associated with dementia, compared with subtype A, in immunosuppressed individuals at risk of cognitive impairment in Kampala, Uganda. Clin Infect Dis 49: 780-786.
33. Frost SD, Wrin T, Smith DM, Kosakovsky Pond SL, Liu Y, et al. (2005) Neutralizing antibody responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infection. Proc Natl Acad Sci U S A 102: 18514-18519.
34. Moore PL, Ranchobe N, Lambson BE, Gray ES, Cave E, et al. (2009) Limited neutralizing antibody specificities drive neutralization escape in early HIV-1 subtype C infection. PLoS Pathog 5: e1000598.
35. McKnight A, Clapham PR, (1995) Immune escape and tropism of HIV. Trends Microbiol 3: 356-361.
36. McKnight A, Weiss RA, Shotton C, Takeuchi Y, Hoshino H, et al. (1995) Change in tropism upon immune escape by human immunodeficiency virus. J Virol 69: 3167-3170.
37. Marcelino J, Borrego P, Rocha C, Barroso H, Quintas A, et al. (2010) Potent and broadly reactive HIV-2 neutralizing antibodies elicited by a Vaccinia virus vector-prime C2V3C3 polypeptide-boost immunization strategy. J Virol.
38. Leitner T, Escanilla D, Marquina S, Wahlberg J, Brostrom C, et al. (1995) Biological and molecular characterization of subtype D, G, and A/D recombinant HIV-1 transmissions in Sweden. Virology 209: 136-146.
39. Sandhu GS, Kline BC, Stockman L, Roberts GD, (1995) Molecular probes for diagnosis of fungal infections. J Clin Microbiol 33: 2913-2919.
40. Carr JK, Salminen MO, Koch C, Gotte D, Artenstein AW, et al. (1996) Full-length sequence and mosaic structure of a human immunodeficiency virus type 1 isolate from Thailand. J Virol 70: 5935-5943.
41. Nicholas KB, Nicholas HB Jr, (1997) GeneDoc: a tool for editing and annotating multiple sequence alignments. Distributed by the author.
42. Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, et al. (1999) Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol 73: 152-160.
43. Felsenstein J, (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17: 368-376.
44. Posada D, Crandall KA, (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817-818.
45. Drummond AJ, Rambaut A, (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7: 214.
46. Abecasis AB, Vandamme AM, Lemey P, (2009) Quantifying differences in the tempo of human immunodeficiency virus type 1 subtype evolution. J Virol 83: 12917-12924.
47. Korber B, Muldoon M, Theiler J, Gao F, Gupta R, et al. (2000) Timing the ancestor of the HIV-1 pandemic strains. Science 288: 1789-1796.
48. Borrego P, Marcelino JM, Rocha C, Doroana M, Antunes F, et al. (2008) The role of the humoral immune response in the molecular evolution of the envelope C2, V3 and C3 regions in chronically HIV-2 infected patients. Retrovirology 5: 78.
49. Sing T, Low AJ, Beerenwinkel N, Sander O, Cheung PK, et al. (2007) Predicting HIV coreceptor usage on the basis of genetic and clinical covariates. Antivir Ther 12: 1097-1106.