Iranian Red Crescent Medical Journal

Published by: Kowsar

Spatio-Temporal Dynamics of HIV-I Subtype B and Circulating Recombinant Form 01_AE Clades in Iran: A Phylogeographic Approach

Sana Eybpoosh 1 , 2 , Abbas Bahrampour 3 , Kayhan Azadmanesh 4 , Ehsan Mostafavi 2 , 5 , Ali Akbar Haghdoost 1 , 6 , * and Farzaneh Zolala 3
Authors Information
1 Regional Knowledge Hub, and WHO Collaborating Centre for HIV/AIDS Surveillance, Institute for Future Studies in Health, Kerman University of Medical Sciences, Kerman, IR Iran
2 Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Hamadan, IR Iran
3 Faculty of public health, Department of Epidemiology and biostatistics, Kerman University of Medical Sciences, Kerman, IR Iran
4 Department of Virology, Pasteur Institute of Iran, Tehran, IR Iran
5 Department of Epidemiology, Pasteur Institute of Iran, Tehran, IR Iran
6 Research Centre for Modeling in Health, Institute for Future Studies in Health, Kerman University of Medical Sciences, Kerman, IR Iran
Article information
  • Iranian Red Crescent Medical Journal: February 01, 2017, 19 (2); e34609
  • Published Online: August 8, 2016
  • Article Type: Research Article
  • Received: November 11, 2015
  • Revised: December 27, 2015
  • Accepted: January 23, 2016
  • DOI: 10.5812/ircmj.34609

To Cite: Eybpoosh S, Bahrampour A, Azadmanesh K, Mostafavi E, Haghdoost A A, et al. Spatio-Temporal Dynamics of HIV-I Subtype B and Circulating Recombinant Form 01_AE Clades in Iran: A Phylogeographic Approach, Iran Red Crescent Med J. 2017 ; 19(2):e34609. doi: 10.5812/ircmj.34609.

Copyright © 2016, Iranian Red Crescent Medical Journal. This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International License ( which permits copy and redistribute the material just in noncommercial usages, provided the original work is properly cited.
1. Background
2. Objectives
3. Methods
4. Results
5. Discussion
  • 1. Sharp PM, Hahn BH. The evolution of HIV-1 and the origin of AIDS. Philos Trans R Soc Lond B Biol Sci. 2010; 365(1552): 2487-94[DOI][PubMed]
  • 2. Angelis K, Albert J, Mamais I, Magiorkinis G, Hatzakis A, Hamouda O, et al. Global Dispersal Pattern of HIV Type 1 Subtype CRF01_AE: A Genetic Trace of Human Mobility Related to Heterosexual Sexual Activities Centralized in Southeast Asia. J Infect Dis. 2015; 211(11): 1735-44[DOI][PubMed]
  • 3. Junqueira DM, de Medeiros RM, Matte MC, Araujo 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): 27489[DOI][PubMed]
  • 4. Carr JK, Salminen MO, Koch C, Gotte D, Artenstein AW, Hegerich PA, et al. Full-length sequence and mosaic structure of a human immunodeficiency virus type 1 isolate from Thailand. J Virol. 1996; 70(9): 5935-43[PubMed]
  • 5. Sarrami-Forooshani R, Das SR, Sabahi F, Adeli A, Esmaeili R, Wahren B, et al. Molecular analysis and phylogenetic characterization of HIV in Iran. J Med Virol. 2006; 78(7): 853-63[DOI][PubMed]
  • 6. Jahanbakhsh F, Ibe S, Hattori J, Monavari SH, Matsuda M, Maejima M, et al. Molecular epidemiology of HIV type 1 infection in Iran: genomic evidence of CRF35_AD predominance and CRF01_AE infection among individuals associated with injection drug use. AIDS Res Hum Retroviruses. 2013; 29(1): 198-203[DOI][PubMed]
  • 7. Foxman B. Molecular Tools and Infectious Disease Epidemiology. 2012;
  • 8. Lemey P, Rambaut A, Drummond AJ, Suchard MA. Bayesian phylogeography finds its roots. PLoS Comput Biol. 2009; 5(9): 1000520[DOI][PubMed]
  • 9. Kuhnert D, Wu CH, Drummond AJ. Phylogenetic and epidemic modeling of rapidly evolving infectious diseases. Infect Genet Evol. 2011; 11(8): 1825-41[DOI][PubMed]
  • 10. Holmes EC. The phylogeography of human viruses. Mol Ecol. 2004; 13(4): 745-56[PubMed]
  • 11. Lemey P, Rambaut A, Welch JJ, Suchard MA. Phylogeography takes a relaxed random walk in continuous space and time. Mol Biol Evol. 2010; 27(8): 1877-85[DOI][PubMed]
  • 12. Hein J, Schierup MH, Wiuf C. Gene Genealogies, Variation and Evolution. 2005;
  • 13. Cabello M, Mendoza Y, Bello G. Spatiotemporal dynamics of dissemination of non-pandemic HIV-1 subtype B clades in the Caribbean region. PLoS One. 2014; 9(8): 106045[DOI][PubMed]
  • 14. Delatorre EO, Bello G. Phylodynamics of HIV-1 subtype C epidemic in east Africa. PLoS One. 2012; 7(7): 41904[DOI][PubMed]
  • 15. Delatorre E, Bello G. Spatiotemporal dynamics of the HIV-1 CRF06_cpx epidemic in Western Africa. AIDS. 2013; 27(8): 1313-20[DOI][PubMed]
  • 16. Paraskevis D, Pybus O, Magiorkinis G, Hatzakis A, Wensing AM, van de Vijver DA, et al. Tracing the HIV-1 subtype B mobility in Europe: a phylogeographic approach. Retrovirology. 2009; 6: 49[DOI][PubMed]
  • 17. Abubakar YF, Meng Z, Zhang X, Xu J. Multiple independent introductions of HIV-1 CRF01_AE identified in China: what are the implications for prevention? PLoS One. 2013; 8(11): 80487[DOI][PubMed]
  • 18. Nerurkar VR, Nguyen HT, Dashwood WM, Hoffmann PR, Yin C, Morens DM, et al. HIV type 1 subtype E in commercial sex workers and injection drug users in southern Vietnam. AIDS Res Hum Retroviruses. 1996; 12(9): 841-3[DOI][PubMed]
  • 19. Kalish ML, Korber BT, Pillai S, Robbins KE, Leo YS, Saekhou A, et al. The sequential introduction of HIV-1 subtype B and CRF01AE in Singapore by sexual transmission: accelerated V3 region evolution in a subpopulation of Asian CRF01 viruses. Virology. 2002; 304(2): 311-29[PubMed]
  • 20. Cohen MS, Chen YQ, McCauley M, Gamble T, Hosseinipour MC, Kumarasamy N, et al. Prevention of HIV-1 infection with early antiretroviral therapy. N Engl J Med. 2011; 365(6): 493-505[DOI][PubMed]
  • 21. Apetrei C, Hahn B, Mizrachi I, Mullins J, Rambaut A, Wolinsky S. Los Alamos Sequence database. Los Alamos HIV databases. 2015;
  • 22. Apetrei C, Hahn B, Mizrachi I, Mullins J, Rambaut A, Wolinsky S. Los Alamos HIV databases. US. 2015;
  • 23. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2009; 37: 26-31[DOI][PubMed]
  • 24. Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006; 22(13): 1658-9[DOI][PubMed]
  • 25. Huang Y, Niu B, Gao Y, Fu L, Li W. CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics. 2010; 26(5): 680-2[DOI][PubMed]
  • 26. Delatorre E, Couto-Fernandez JC, Guimaraes ML, Vaz Cardoso LP, de Alcantara KC, Stefani MM, et al. Tracing the origin and northward dissemination dynamics of HIV-1 subtype C in Brazil. PLoS One. 2013; 8(9): 74072[DOI][PubMed]
  • 27. Marcus U, Schmidt AJ, Kollan C, Hamouda O. The denominator problem: estimating MSM-specific incidence of sexually transmitted infections and prevalence of HIV using population sizes of MSM derived from Internet surveys. BMC Public Health. 2009; 9: 181[DOI][PubMed]
  • 28. Strimmer K, von Haeseler A. Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment. Proc Natl Acad Sci U S A. 1997; 94(13): 6815-9[PubMed]
  • 29. Ackermann M, Strimmer K. A general modular framework for gene set enrichment analysis. BMC Bioinformatics. 2009; 10: 47[DOI][PubMed]
  • 30. Lemey P, Salemi M, Vandamme AM. The phylogenetic handbook: a practical approach to phylogenetic analysis and hypothesis testing. 2009;
  • 31. Tee KK, Pybus OG, Li XJ, Han X, Shang H, Kamarulzaman A, et al. Temporal and spatial dynamics of human immunodeficiency virus type 1 circulating recombinant forms 08_BC and 07_BC in Asia. J Virol. 2008; 82(18): 9206-15[DOI][PubMed]
  • 32. Hasegawa M, Kishino H, Yano T. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol. 1985; 22(2): 160-74[PubMed]
  • 33. Bello G, Afonso JM, Morgado MG. Phylodynamics of HIV-1 subtype F1 in Angola, Brazil and Romania. Infect Genet Evol. 2012; 12(5): 1079-86[DOI][PubMed]
  • 34. Veras NM, Gray RR, Brigido LF, Rodrigues R, Salemi M. High-resolution phylogenetics and phylogeography of human immunodeficiency virus type 1 subtype C epidemic in South America. J Gen Virol. 2011; 92: 1698-709[DOI][PubMed]
  • 35. Faria NR, Rambaut A, Suchard MA, Baele G, Bedford T, Ward MJ, et al. HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations. Science. 2014; 346(6205): 56-61[DOI][PubMed]
  • 36. Naderi HR, Tagliamonte M, Tornesello ML, Ciccozzi M, Rezza G, Farid R, et al. Molecular and phylogenetic analysis of HIV-1 variants circulating among injecting drug users in Mashhad-Iran. Infect Agent Cancer. 2006; 1: 4[DOI][PubMed]
  • 37. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol. 2013; 30(12): 2725-9[DOI][PubMed]
  • 38. Larsson A. AliView: a fast and lightweight alignment viewer and editor for large datasets. Bioinformatics. 2014; 30(22): 3276-8[DOI][PubMed]
  • 39. Schmidt HA, Strimmer K, Vingron M, von Haeseler A. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics. 2002; 18(3): 502-4[PubMed]
  • 40. Drummond AJ, Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 2007; 7: 214[DOI][PubMed]
  • 41. Suchard MA, Rambaut A. Many-core algorithms for statistical phylogenetics. Bioinformatics. 2009; 25(11): 1370-6[DOI][PubMed]
  • 42. Rambaut A, Drummond A. LogCombiner v1.8.1. 2002-2014;
  • 43. Rambaut A, Drummond A. Tracer v1.4. 2007;
  • 44. Rambaut A, Drummond A. TreeAnnotator v1.8.1. 2002-2014;
  • 45. Rambaut A. FigTree v1.4: Tree Figure Drawing Tool. 2009;
  • 46. Bielejec F, Rambaut A, Suchard MA, Lemey P. SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics. Bioinformatics. 2011; 27(20): 2910-2[DOI][PubMed]
  • 47. Motevalian SA, Jahani M, Mahmoodi M. Driving under influence of opiates in heavy vehicle drivers of Iran in 2001. Hakim Res J. 2004; 7(1): 1-8
  • 48. Delany-Moretlwe S, Bello B, Kinross P, Oliff M, Chersich M, Kleinschmidt I, et al. HIV prevalence and risk in long-distance truck drivers in South Africa: a national cross-sectional survey. Int J STD AIDS. 2014; 25(6): 428-38[DOI][PubMed]
  • 49. Baltazar CS, Horth R, Inguane C, Sathane I, Cesar F, Ricardo H, et al. HIV prevalence and risk behaviors among Mozambicans working in South African mines. AIDS Behav. 2015; 19 Suppl 1-67[DOI][PubMed]
  • 50. Frost SD, Volz EM. Viral phylodynamics and the search for an 'effective number of infections'. Philos Trans R Soc Lond B Biol Sci. 2010; 365(1548): 1879-90[DOI][PubMed]
  • 51. Volz EM, Kosakovsky Pond SL, Ward MJ, Leigh Brown AJ, Frost SD. Phylodynamics of infectious disease epidemics. Genetics. 2009; 183(4): 1421-30[DOI][PubMed]
  • 52. Faria NR, Suchard MA, Abecasis A, Sousa JD, Ndembi N, Bonfim I, et al. Phylodynamics of the HIV-1 CRF02_AG clade in Cameroon. Infect Genet Evol. 2012; 12(2): 453-60[DOI][PubMed]
  • 53. Bello G, Aulicino PC, Ruchansky D, Guimaraes ML, Lopez-Galindez C, Casado C, et al. Phylodynamics of HIV-1 circulating recombinant forms 12_BF and 38_BF in Argentina and Uruguay. Retrovirology. 2010; 7: 22[DOI][PubMed]
  • 54. Foster GM, Ambrose JC, Hue S, Delpech VC, Fearnhill E, Abecasis AB, et al. Novel HIV-1 recombinants spreading across multiple risk groups in the United Kingdom: the identification and phylogeography of Circulating Recombinant Form (CRF) 50_A1D. PLoS One. 2014; 9(1): 83337[DOI][PubMed]
  • 55. Mumtaz GR, Riedner G, Abu-Raddad LJ. The emerging face of the HIV epidemic in the Middle East and North Africa. Curr Opin HIV AIDS. 2014; 9(2): 183-91[DOI][PubMed]
  • 56. Islamic Republic of Iran AIDS progress report. 2014;
  • 57. Haghdoost AA, Mostafavi E, Mirzazadeh A, Navadeh S, Feizzadeh A, Fahimfar N. Modelling of HIV/AIDS in Iran up to 2014. J AIDS HIV Res. 2011; 3(12)[DOI]
  • 58. Apetrei C, Hahn B, Mizrachi I, Mullins J, Rambaut A, Wolinsky S. HIV Circulating Recombinant Forms (CRFs). 2015;
Creative Commons License Except where otherwise noted, this work is licensed under Creative Commons Attribution Non Commercial 4.0 International License .

Search Relations:



Create Citiation Alert
via Google Reader

Readers' Comments