medigraphic.com
ISSN 1527-3172 (Electronic)

2017, Number 2-3

<< Back Next >>

MEDICC Review 2017; 19 (2-3)

Origin and evolutionary history of HIV-1 subtype B in Cuba

Machado-Zaldívar LY, Díaz-Torres HM, Blanco-de Armas M, Romay-Franchy D, Dubed-Echevarría M

Language: English
References: 46
Page: 40-44
PDF size: 169.16 Kb.


ABSTRACT

Introduction Cuba’s HIV epidemic is characterized by high genetic diversity, with circulation of several subtypes and recombinant forms. Earlier studies described a predominance of subtype B in the HIV-positive population, but these studies did not take into account patients’ epidemiologic history.
Objective Clarify the origin and phylodynamics of HIV-1 subtype B in the Cuban epidemic.
Methods We analysed phylogenetic relationships among 120 sequences (from different geographic origins) of the pol gene in HIV-1 subtype B isolates from Cuban patients diagnosed from 1987 through 2012. Time of HIV-1 subtype B introduction and viral evolutionary rate were determined using a Bayesian coalescent method.
Results Based on phylogenetic relationships, subtype B was introduced into Cuba multiple times. Subtype B spread in Cuba through dissemination of strains that probably came from the USA, Canada and Europe. The time of the most recent common ancestor of Cuban subtype B was close to 1977 (95% CI 1974–1982), and the evolutionary rate was 2.7 x 10-3 nucleotide substitutions per site per year.
Conclusions Our results suggest multiple introductions of HIV-1B into Cuba in the late 1970s, predominantly strains from North America and Europe. The results reflect the importance of maintaining, reviewing and updating molecular epidemiology of HIV-1 in Cuba, due to its rapid evolution and possible implications for the National STI/HIV/AIDS Program of Cuba’s Ministry of Public Health.


REFERENCES

  1. Worobey M, Gemmel M, Teuwen DE, Haselkorn T, Kunstman K, Bunce M, et al. Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960. Nature. 2008 Oct 2;455(7213):661–4.

  2. Sharp PM, Hahn BH. The evolution of HIV-1 and the origin of AIDS. Philos Trans R Soc Lond B Biol Sci. 2010 Aug 27;365(1552):2487–94.

  3. Faria NR, Rambaut A, Suchard M, Baele G, Bedford T, Ward MJ, et al. The early spread and epidemic ignition of HIV-1 in human populations. Science. 2014 Oct 3;346(6205):56–61.

  4. Tongo M, Dorfman JR, Martin DP. High degree of HIV-1 group M (HIV-1M) genetic diversity within circulating recombinant forms: insight into the early events of HIV-1M evolution. J Virol. 2015 Dec 9;90(5):2221–9.

  5. Barre-Sinoussi F, Chermann JC, Rey F, Nugeyre MT, Chamaret S, Gruest T, et al. Isolation of a T-lymphotropic retrovirus from a patient at risk for AIDS. Science. 1983 May 20;220(4599):868–71.

  6. Montagnier L, Chermann JC, Barr-Sinoussi F. A new human T-lymphotropic retroviruses: characterization and possible role in lymphadenophaty and acquired immunodefi ciency syndromes. In: Gallo RC, Essex ME, Gross L, editors. Human T-cell leukemia/lymphoma virus: the family of human T-lymphotropic retroviruses: their role in malignancies and association with AIDS. New York: Cold Spring Harbor Laboratory Press; 1984. p. 363–79.

  7. Junqueira DM, Almeida SE. HIV-1 subtype B: Traces of a pandemic. Virology. 2016 Aug;495:173–84.

  8. Cabello M, Mendoza Y, Bello G. Spatiotemporal dynamics of dissemination of pandemic HIV-1 subtype B clades in the Caribbean. PLoS One. 2014 Aug 22;9(8):e106045.

  9. Chalmet K, Staelens D, Blot S, Dinakis S, Pelgrom J, Plum J, et al. Epidemiological study of phylogentic transmission clusters in a local HIV- 1 epidemic reveals distinct differences between subtype B and non-B infections. BMC Infect Dis. 2010 Sep 7;10:262.

  10. Magiorkibis G, Angelis K, Mamais I, Katzourakis A, Hatzakis A, Albert J, et al. The global spread of HIV-1 subtype B epidemic. Infect Genet Evol. 2016 Dec 46;169–79.

  11. Rolo F, Miranda L, Wainberg M, Gu Z, Lobaina L, Noa E, et al. Envelope V3 Region Sequences of Cuban HIV-1 Isolates. J Acquir Immune Defi c Syndr Hum Retrovirol. 1995 Jun 1;9(2):123–5.

  12. Gómez C, Iglesias E, Perdomo W, Rolo F, Blanco M, Lobaina L, et al. Isolates from four different HIV type 1 clades circulating in Cuba. Identifi ed by DNA sequence of the C2–V3 region. AIDS Res Hum Retroviruses. 2001 Jan 1;17(1):55–8.

  13. Cuevas MT, Ruibal I, Villahermosa ML, Díaz H, Delgado E, Parga EV, et al. High HIV-1 genetic diversity in Cuba. AIDS. 2002 Aug 16;16(12):1643–53.

  14. Pérez L, Thomson MM, Bleda MJ, Aragonés C, González Z, Pérez J, et al. HIV Type 1 molecular epidemiology in Cuba: high genetic diversity, frequent mosaicism, and recent expansion of BG intersubtype recombinant forms. AIDS Res Hum Retroviruses. 2006 Aug;22(8):724–33.

  15. Machado LY, Blanco M, Dubed M, Díaz HM, Ruiz NM, Valdés N, et al. HIV type 1 genetic diversity in newly diagnosed Cuban patients. AIDS Res Hum Retroviruses. 2012 Aug;28(8):956–60.

  16. Machado LY, Dubed M, Díaz HM, Ruiz NM, Romay D, Valdés N, et al. Transmitted HIV type 1 drug resistance in newly diagnosed Cuban patients. AIDS Res Hum Retroviruses. 2013 Feb;29(2):411–4.

  17. Kourí V, Alemán Y, Pérez L, Pérez J, Fonseca C, Correa C, et al. High frequency of antiviral drug resistance and non-B subtypes in HIV-1 patients failing antiviral therapy in Cuba. J Clin Virol. 2012 Dec;55(4):348–55.

  18. Pérez L, Kourí V, Alemán Y, Abrahantes Y, Correa C, Aragonés C, et al. Antiretroviral drug resistance in HIV-1 therapy-naive patients in Cuba. Infect Genet Evol. 2013 Jun;16:144–50.

  19. Junqueira DM, de Medeiros RM, Matte MC, Araújo LA, Chies JA, Ashton-Prolla P, et al. Reviewing the history of HIV-1: spread of subtype B in the Americas. PLoS One. 2011;6(11):e27489.

  20. Pagán I, Holguín A. Reconstructing the timing and dispersion routes of HIV-1 subtype B epidemics in the Caribbean and Central America: a phylogenetic story. PLoS One. 2013;8(7):e69218.

  21. Delatorre E, Bello G. Phylodynamics of the HIV-1 epidemic in Cuba. PLoS One. 2013 Jul 9;8(7):e72448.

  22. Los Alamos National Laboratory HIV-AIDS Databases [Internet]. New Mexico: Los Alamos National Laboratory; c2005–2017 [cited 2013 Jan 29]. Available from: http://www.hiv.lanl.gov

  23. Hall TA. Bioedit: a user-friendly biological sequence aligment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser. 1999;41:95–8.

  24. Kimura M. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 1980 Dec;16(2):111–20.

  25. Tamura KD, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA 5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011 Oct;28(10):2731–9.

  26. Drummond AJ, Suchard MA, Xie D, Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. 2012 Aug;29(8):1969–73.

  27. Drummond AJ, Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 2007 Nov 8;7:214.

  28. World Medical Association [Internet]. Ferney- Voltaire (FR): World Medical Association; c2017. Helsinki Declaration. Ethical principles for medical research involving human subjects. 59nd General Assembly, Seul, Korea; 2008 Oct [cited 2017 Mar 22]. Available from: https://www.wma .net/policies-post/wma-declaration-of-helsinki -ethical-principles-for-medical-research-invol ving-human-subjects/

  29. Grabowski MK, Redd AD. Molecular tools for studying HIV transmission in sexual networks. Curr Opin HIV AIDS. 2014 Mar;9(2):126–33.

  30. Blanco M, Machado LY, Díaz HM, Ruiz N, Romay D, Silva E. HIV-1 genetic variability in Cuba and implications for transmission and clinical progression. MEDICC Rev. 2015 Oct;17(4):25–31.

  31. Machuca R, Jorgensen LB, Theilade P, Nielsen C. Molecular investigation of transmission of Human Immunodefi ciency Virus type I in a criminal case. Clin Diagn Lab Immunol. 2001 Sep;8(5):884–90.

  32. Gilbert MT, Rambaut A, Wlasiuk G, Spira TJ, Pitchenik AE, et al. The emergence of HIV/AIDS in the Americas and beyond. Proc Natl Acad Sci USA. 2007 Nov 20;104(47):18566-70.

  33. Center for Disease Control (CDC). Pneumocystis carinii pneumonia – Los Angeles. MMWR. 1981 Jun;30(21):250–2.

  34. Buchbinder SP, Katz MH, Hessal NA, O´Malley PM, Holmberg SD. Long term HIV-1 infection without immunologic progression. AIDS. 1994 Aug;8(8):1123–8.

  35. Ruibal-Brunet IJ, Cuevas MT, Díaz-Torres H, Villahermosa ML, Noa-Romero E, Vázquez de Parga E, et al. Genotypic resistance mutations to antiretroviral drugs in HIV-1 B and non-B subtypes from Cuba. Rev Panam Salud Pública. 2001 Sep;10(3):174–80.

  36. Hué S, Clewey JP, Cane PA, Pillay D. HIV-1 pol gene variation is suffi cient for reconstruction of transmissions in the era of antiretroviral therapy. AIDS. 2004 Mar 26;18(5):719–28.

  37. Yebra G, Holguín A, Pillay D, Hué S. Phylogenetic and demographic characterization of HIV-1 transmission in Madrid, Spain. Infect Genet Evol. 2013 Mar;14:232–9.

  38. Pagán I, Holmes EC. Long-term evolution of the Luteoviridae: Time scale and mode of virus speciation. J Virol. 2010 Jun;84(12):6177–87.

  39. Hué S, Pillay D, Clewley JP, Pybus OG. Genetic analysis reveals the complex structure of HIV-1 transmission within defi ned risk groups. Proc Natl Acad Sci USA. 2005 Mar 22;102(12):4425–9.

  40. Hué S, Gifford RJ, Dunn D, Fernhill E, Pillay D; UK Collaborative Group on HIV Drug Resistance. Demonstration of sustained drug-resistant human immunodefi ciency virus type 1 lineages circulating among treatment-naive individuals. J Virol. 2009 Mar;83(6):2645–54.

  41. Salemi M, de Oliveira T, Ciccozzi M, Rezza G, Goodenow MM. High-resolution molecular epidemiology and evolutionary history of HIV-1 subtypes in Albania. PLoS One. 2008 Jan 2;3(1):e1390. DOI: 10.1371/journal. pone.0001390.

  42. Kim GJ, Yun MR, Koo MJ, Shin BG, Lee JS, Kim SS. Estimating the origin an evolution characteristics for Korean HIV type 1 subtype B using Bayesian phylogenetic analysis. AIDS Res Hum Retroviruses. 2012 Aug;28(8):880–4.

  43. Freed EO, Mouland AJ. The cell biology of HIV-1 and other retroviruses. Retrovirology. 2006 Nov 3;3:77.

  44. Nei M, Kumar S. Molecular Evolution and Phylogenetics. Oxford: Oxford University Press; 2000.

  45. Ceccherini-Silberstein F, Gago F, Santoro M, Gori C, Svicher V, Rodríguez-Barrios F, et al. High sequence conservation of human immunodefi ciency virus type 1 reverse transcriptase under drug pressure despite the continuous appearance of mutations. J Virol. 2005 Aug;79(16):10718–9.

  46. Santos AFA, Lenbruger RB, Soares EA, Jere A, Sprinz E, Martínez AM, et al. Conservation patterns of HIV-1 RT connection and Rnase H domains: Identifi cation of new mutations in NRTI-treated patients. PLoS One. 2008 Mar 12;3(3):e1781. DOI: 10.1371/journal. pone.0001781.




2020     |     www.medigraphic.com