Molecular surveillance of HIV-1 in Madrid, Spain: A phylogeographic analysis

Journal of Virology

Volumn 85, Issue 20, 2011, Pages 10755-10763

  González Alba, José M ^a,b   Holguín, Africa ^a,b   Garcia, Rosa ^c   García Bujalance, Silvia ^d   Alonso, Roberto ^e   Suárez, Avelina ^f   Delgado, Rafael ^g   Cardeñoso, Laura ^h   González, Rosa ⁱ   García Bermejo, Isabel ^j   Portero, Francisca ^k   de Mendoza, Carmen ^d   González Candelas, Fernando ^b,l   Galán, Juan Carlos ^a,b,m  

^a INSTITUTO RAMÓN Y CAJAL DE INVESTIGACIÓN SANITARIA IRYCIS   (Spain)

^b CIBER EPIDEMIOLOGÍA Y SALUD PÚBLICA CIBERESP   (Spain)

^c Hospital UniversitarioFundación Jiménez Díaz   (Spain)

^d HOSPITAL UNIVERSITARIO LA PAZ   (Spain)

^e HOSPITAL GENERAL UNIVERSITARIO GREGORIO MARAÑÓN   (Spain)

^f HOSPITAL CLÍNICO SAN CARLOS   (Spain)

^g HOSPITAL UNIVERSITARIO 12 DE OCTUBRE   (Spain)

^h HOSPITAL UNIVERSITARIO DE LA PRINCESA   (Spain)

ⁱ HOSPITAL UNIVERSITARIO PRÍNCIPE DE ASTURIAS   (Spain)

^j HOSPITAL UNIVERSITARIO DE GETAFE   (Spain)

^k HOSPITAL UNIVERSITARIO PUERTA DE HIERRO   (Spain)

^l UNIVERSITY OF VALENCIA   (Spain)

^m CSIC   (Spain)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CAUCASIAN; CLUSTER ANALYSIS; COHORT ANALYSIS; CONTROLLED STUDY; ETHNIC GROUP; GENE SEQUENCE; HISPANIC; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; IMMIGRANT; IMMIGRATION; MAJOR CLINICAL STUDY; MOLECULAR EPIDEMIOLOGY; NEGRO; NUCLEOTIDE SEQUENCE; PHYLOGEOGRAPHY; PREVALENCE; PRIORITY JOURNAL; RUSSIAN; SPAIN; STRUCTURAL GENE; URBAN AREA; VIRUS IDENTIFICATION; VIRUS RECOMBINANT; VIRUS TRANSMISSION;

CLUSTER ANALYSIS; GENOTYPE; HIV INFECTIONS; HIV-1; HUMANS; MOLECULAR EPIDEMIOLOGY; MOLECULAR SEQUENCE DATA; PHYLOGEOGRAPHY; POL GENE PRODUCTS, HUMAN IMMUNODEFICIENCY VIRUS; POPULATION GROUPS; PREVALENCE; SEQUENCE ANALYSIS, DNA; SPAIN; TRANSIENTS AND MIGRANTS;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 80054980896     PISSN: 0022538X     EISSN: 10985514     Source Type: Journal    
DOI: 10.1128/JVI.00454-11     Document Type: Article

References (58)

1. Anisimova, M., and O. Gascuel. 2006. Approximate likelihood ratio test for branches: a fast, accurate and powerful alternative. Syst. Biol. 55:539-552.
2. Apetrei, C., et al. 1997. HIV type 1 subtype F sequences in Romanian children and adults. AIDS Res. Hum. Retroviruses 13:363-365.
3. Aulicino, P. C., E. C. Holmes, C. Rocco, A. Mangano, and L. Sen. 2007. Extremely rapid spread of human immunodeficiency virus type 1 BF recombinants in Argentina. J. Virol. 81:427-429.
4. Bártolo, I., et al. 2009. Highly divergent subtypes and new recombinant forms prevail in the HIV/AIDS epidemic in Angola: new insights into the origins of the AIDS pandemic. Infect. Genet. Evol. 9:672-682.
5. Bruselles, A., G. Rozera, B. Bartolini, M. Prosperi, and F. del Nonno. 2009. Use of massive parallel pyrosequencing for near full-length characterization of a unique HIV type 1 BF recombinant associated with a fatal primary infection. AIDS Res. Hum. Retroviruses 25:937-942.
6. Buonaguro, L., M. Tagliamonte, M. L. Tornesello, and F. M. Buonaguro. 2007. Genetic and phylogenetic evolution of HIV-1 in a low subtype heterogeneity epidemic: the Italian example. Retrovirology 4:34.
7. Cuevas, M. T., et al. 2009. Incidence of non-B subtypes of HIV-1 in Galicia, Spain: high frequency and diversity of HIV-1 among men who have sex with men. Euro Surveill. 14:19413.
8. Delgado, E., et al. 2010. Identification of a new HIV type 1 BF intersubtype circulating recombinant form (CRF44_BF) in Chile. AIDS Res. Hum. Retroviruses 26:821-826.
9. Delgado, E., 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.
10. de Oliveira, T., D. Pillay, R. J. Gifford and the U.K. Collaborative Group on HIV Drug Resistance. 2010. The HIV-1 subtype C epidemic in South America is linked to the United Kingdom. PLoS One 5:e9311.
11. Derache, A., et al. 2008. Evolution of genetic diversity and drug resistance mutations in HIV-1 among untreated patients from Mali between 2005 and 2006. J. Antimicrob. Chemother. 62:456-463.
12. Fernández-García, A., et al. 2010. Identification of a new HIV type 1 circulating BF intersubtype recombinant form (CRF47_BF) in Spain. AIDS Res. Hum. Retroviruses 26:827-832.
13. Gao, F., et al. 1996. The heterosexual human immunodeficiency virus type 1 epidemic in Thailand is caused by an intersubtype (A/E) recombinant of African origin. J. Virol. 70:7013-7029.
14. Geretti, A. M. 2006. HIV-1 subtypes: epidemiology and significance for HIV management. Curr. Opin. Infect. Dis. 19:1-7.
15. Gifford, R. J., et al. 2007. Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of human immunodeficiency virus type 1. J. Virol. 81:13050-13056.
16. Guimarães, M. L., et al. 2009. Close phylogenetic relationship between Angolan and Romanian HIV-1 subtype F1 isolates. Retrovirology 6:39.
17. Guindon, S., and O. Gascuel. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704.
18. Hamers, F. F., and A. M. Downs. 2004. The changing face of the HIV epidemic in Western Europe: what are the implications for public health policies? Lancet 364:83-94.
19. Heath, L., E. van der Walt, A. Varsani, and D. P. Martin. 2006. Recombination patterns in aphthoviruses mirror those found in other picornaviruses. J. Virol. 80:11827-11832.
20. Hemelaar, J., E. Gouws, P. D. Ghys, and S. Osmanov. 2006. Global and regional distribution of HIV-1 genetic subtypes and recombinants in 2004. AIDS 20:W13-W23.
21. Herm, A. 2008. Recent migration trends: citizens of EU-27 member states become ever more mobile while EU remains attractive to non-EU citizens. EUROSTAT: Statistics in focus 98/2008. http://epp.eurostat.ec.europa.eu/cache/ity_offpub/ks-sf-08-098-en/ks-sf-08-098-en.pdf.
22. Holguín, A., A. Alvarez, and V. Soriano. 2002. High prevalence of HIV-1 subtype G and natural polymorphisms at the protease gene among HIVinfected immigrants in Madrid. AIDS 16:1163-1170.
23. Holguín, A., M. Mulder, G. Yebra, M. López, and V. Soriano. 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.
24. Holguín, A., M. J. Pena, F. Troncoso, and V. Soriano. 2007. Introduction of non-B subtypes among Spaniards newly diagnosed with HIV type 1 in the Canary Islands. AIDS Res. Hum. Retroviruses 23:498-502.
25. Holmes, E. C. 2007. When HIV spread afar. Proc. Natl. Acad. Sci. U. S. A. 104:18351-18352.
26. Jere, A., S. Tripathy, K. Agnihotri, S. Jadhav, and R. Paranjape. 2004. Genetic analysis of Indian HIV-1 nef: subtyping, variability and implications. Microbes Infect. 6:279-289.
27. Jetzt, A. E., et al. 2000. High rate of recombination throughout the human immunodeficiency virus type 1 genome. J. Virol. 74:1234-1240.
28. Kalish, M. L., et al. 2004. Recombinant viruses and early global HIV-1 epidemic. Emerg. Infect. Dis. 10:1227-1234.
29. Konings, F., et al. 2006. Genetic analysis of HIV-1 strains in rural Eastern Cameroon indicates the evolution of second-generation recombinants to circulating recombinant forms. J. Acquir. Immune Defic. Syndr. 42:331-341.
30. Lewis, F., G. J. Hughes, A. Rambaut, A. Pozniak, and Leigh A. J. Brown. 2008. Episodic sexual transmission of HIV revealed by molecular phylodynamics. PLoS Med. 5:e50. doi:10.1371/journal.pmed.0050050.
31. Mansky, L. M., and H. M. Temin. 1995. Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase. J. Virol. 69:5087-5094.
32. McConnell, M. J., et al. 2008. Molecular epidemiology of HIV type 1 in newly diagnosed patients in southern Spain. AIDS Res. Hum. Retroviruses 24:881-887.
33. Moore, C. B., et al. 2002. Evidence of HIV-1 adaptation to HLA-restricted immune responses at a population level. Science 296:1439-1443.
34. Muñoz-Nieto, M., et al. 2008. HIV type 1 intersubtype recombinants during the evolution of a dual infection with subtypes B and G. AIDS Res. Hum. Retroviruses 24:337-343.
35. Paraskevis, D., et al. 2009. Tracing the HIV-1 subtype B mobility in Europe: a phylogeographic approach. Retrovirology 6:49.
36. Parczewski, M., et al. 2010. Characteristics of HIV-1 non-B subtype infections in Northwest Poland. J. Med. Virol. 82:1306-1313.
37. Perelson, A. S., A. U. Neumann, M. Markowitz, J. M. Leonard, and D. D. Ho. 1996. HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time Science 271:1582-1586.
38. Pérez-Alvarez, L., 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.
39. Perrin, L., L. Kaiser, and S. Yerly. 2003. Travel and the spread of HIV-1 genetic variants. Lancet Infect. Dis. 3:22-27.
40. Plantier, J. C., et al. 2009. A new human immunodeficiency virus derived from gorillas. Nat. Med. 15:871-872.
41. Posada, D. 2008. jModelTest: phylogenetic model averaging. Mol. Biol. Evol. 25:1253-1256.
42. Rambaut, A., D. Posada, K. A. Crandall, and E. C. Holmes. 2004. The causes and consequences of HIV evolution. Nat. Rev. Genet. 5:52-61.
43. Ruchansky, D., C. Casado, J. Russi, J. Rabiza, and C. López-Galindez. 2009. Identification of a new HIV-1 circulating recombinant form (CRF38_BF1) in Uruguay. AIDS Res. Hum. Retroviruses 25:351-356.
44. Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
45. Sax, P. E., et al. 2005. Should resistance testing be performed for treatmentnaive HIV-infected patients? A cost-effectiveness analysis. Clin. Infect. Dis. 41:1316-1323.
46. Sierra, M., et al. 2007. Identification of 3 phylogenetically related HIV-1 BG intersubtype circulating recombinant forms in Cuba. J. Acquir. Immune Defic. Syndr. 45:151-160.
47. Soares, E. A., et al. 2005. HIV-1 subtype C dissemination in southern Brazil. AIDS 19(Suppl. 4):S81-S86.
48. Soares, M. A., et al. 2003. A specific subtype C of human immunodeficiency virus type 1 circulates in Brazil. AIDS 17:11-21.
49. Tatt, I. D., K. L. Barlow, J. P. Clewley, O. N. Gill, and J. V. Parry. 2004. Surveillance of HIV-1 subtypes among heterosexuals in England and Wales, 1997-2000. J. Acquir. Immune Defic. Syndr. 36:1092-1099.
50. Taylor, B. S., M. E. Sobieszczyk, F. E. McCutchan, and S. M. Hammer. 2008. The challenge of HIV-1 subtype diversity. N. Engl. J. Med. 358:1590-1602.
51. van der Kuyl, A. C., and M. Cornelissen. 2007. Identifying HIV-1 dual infections. Retrovirology 4:67.
52. Vasileva, K. 2009. Citizens of European countries account for the majority of the foreign population in EU-27 in 2008. EUROSTAT: Statistics in focus 94/2009. http://epp.eurostat.ec.europa.eu/cache/ity_offpub/ks-sf-09-094/en/ks-sf-09-094-en.pdf.
53. Vidal, N., et al. 2000. Unprecedented degree of human immunodeficiency virus type 1 (HIV-1) group M genetic diversity in the Democratic Republic of Congo suggests that the HIV-1 pandemic originated in Central Africa. J. Virol. 74:10498-10507.
54. Wheeler, W. H., et al. 2010. Prevalence of transmitted drug resistance associated mutations and HIV-1 subtypes in new HIV-1 diagnoses, U.S.-2006. AIDS 24:1203-1212.
55. Worobey, M., et al. 2008. Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960. Nature 455:661-664.
56. Yamaguchi, J., et al. 2008. Identification of new CRF43_02G and CRF25_cpx in Saudi Arabia based on full genome sequence analysis of six HIV type 1 isolates. AIDS Res. Hum. Retroviruses 24:1327-1335.
57. Yirrell, D. L., et al. 2008. HIV subtypes in Scotland, 2000-2006. Epidemiol. Infect. 136:1069-1075.
58. Zhang, M., et al. 2010. The role of recombination in the emergence of a complex and dynamic HIV epidemic. Retrovirology 7:25.