Molecular analysis and phylogenetic characterization of HIV in Iran

Journal of Medical Virology

Volumn 78, Issue 7, 2006, Pages 853-863

  Sarrami Forooshani, Ramin ^a   Das, Suman Ranjan ^b   Sabahi, Farzaneh ^a   Adeli, Ahmad ^a   Esmaeili, Rezvan ^a   Wahren, Britta ^c   Mohraz, Minoo ^d   Haji Abdolbaghi, Mahboubeh ^d   Rasoolinejad, Mehrnaz ^d   Jameel, Shahid ^b   Mahboudi, Fereidoun ^a  

^a PASTEUR INSTITUTE OF IRAN   (Iran)

^b INTERNATIONAL CENTRE FOR GENETIC ENGINEERING AND BIOTECHNOLOGY ICGEB   (India)

^c KAROLINSKA INSTITUTE   (Sweden)

^d TEHRAN UNIVERSITY OF MEDICAL SCIENCES   (Iran)

Author keywords

AIDS; Hemophiliacs; HIV 1; Injecting drug users; Iran; Molecular epidemiology

Indexed keywords

ADULT; ARTICLE; ENVELOPE GENE; EPIDEMIC; FEMALE; GENE SEQUENCE; GENETIC DISTANCE; HEMOPHILIA; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; INTRAVENOUS DRUG ABUSE; IRAN; MAJOR CLINICAL STUDY; MALE; MOLECULAR CLONING; MOLECULAR EPIDEMIOLOGY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ANALYSIS; STRUCTURAL GENE; UNINDEXED SEQUENCE; VIRUS TYPING;

AMINO ACID SEQUENCE; CLONING, MOLECULAR; DISEASE OUTBREAKS; EPIDEMIOLOGY, MOLECULAR; GENE PRODUCTS, GAG; GENES, ENV; GENES, GAG; GENOTYPE; HEMOPHILIA A; HIV ANTIGENS; HIV INFECTIONS; HIV-1; HUMANS; IRAN; MALE; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE HOMOLOGY, AMINO ACID; SUBSTANCE ABUSE, INTRAVENOUS; VARIATION (GENETICS); VIRAL PROTEINS;

CERCOPITHECINE HERPESVIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 33744979754     PISSN: 01466615     EISSN: 10969071     Source Type: Journal    
DOI: 10.1002/jmv.20634     Document Type: Article

References (45)

1. Arnold C, Barlow KL, Kaye S, Loveday C, Balfe P, Clewley JP. 1995. HIV type 1 sequence subtype G transmission from mother to infant: Failure of variant sequence species to amplify in the Roche Amplicor Test. AIDS Res Hum Retroviruses 11:999-1001.
2. Ayehunie S, Johansson B, Salminen M, Leinikki P, Sonnerborg A, Zewdie DW, Britton S, Strannegard O. 1991. HIV-1 in Ethiopia: Phylogenetic divergence from other HIV-1 strains. Virus Genes 5:359-366.
3. Becker ML, De JG, Becker WB. 1995. Analysis of partial gag and env gene sequences of HIV type 1 strains from southern Africa. AIDS Res Hum Retroviruses 11:1265-1267.
4. Bobkov A, Kazennova E, Selimova L, Bobkova M, Khanina T, Ladnaya N, Kravchenko A, Pokrovsky V, Cheingsong-Popov R, Weber J. 1998. A sudden epidemic of HIV type 1 among injecting drug users in the former Soviet Union: Identification of subtype A, subtype B, and novel gagA/envB recombinants. AIDS Res Hum Retroviruses 14:669-676.
5. Buonaguro L, Del GE, Monaco M, Greco D, Corti P, Beth-Giraldo E, Buonaguro FM, Giraldo G. 1995. Heteroduplex mobility assay and phylogenetic analysis of V3 region sequences of human immunodeficiency virus type 1 isolates from Gulu, northern Uganda: The Italian-Ugandan Cooperation AIDS Program. J Virol 69:7971-7981.
6. Burke D, McCutchan FE. 1997. Global distribution of human immunodeficiency virus-1 clades. In: D.V.J. Vincent T, Hellman S, Rosenberg SA, editors. AIDS: Biology, diagnosis, treatment, and prevention. Philadelphia: Lippincott-Raven. pp 119-126.
7. De Jong JJ, De RA, 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.
8. Derdeyn CA, Decker JM, Bibollet-Ruche F, Mokili JL, Muldoon M, Denham SA, Heil ML, Kasolo F, Musonda R, Hahn BH, Shaw GM, Korber BT, Allen S, Hunter E. 2004. Envelope-constrained neutralization-sensitive HIV-1 after heterosexual transmission. Science 303:2019-2022.
9. Fouchier RA, Groenink M, Kootstra NA, Tersmette M, Huisman HG, Miedema F, Schuitemaker H. 1992. Phenotype-associated sequence variation in the third variable domain of the human immunodeficiency virus type 1 gp120 molecule. J Virol 66:3183-3187.
10. Gao F, Vidal N, Li Y, Trask SA, Chen Y, Kostrikis LG, Ho DD, Kim J, Oh MD, Choe K, Salminen M, Robertson DL, Shaw GM, Hahn BH, Peeters M. 2001. Evidence of two distinct subsubtypes within the HIV-1 subtype A radiation. AIDS Res Hum Retroviruses 17:675-688.
11. Hall TA. 1999. BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41:95-98.
12. Ho DD, Neumann AU, Perelson AS, Chen W, Leonard JM, Markowitz M. 1995. Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection. Nature 373:123-126.
13. Iranian Disease Management Center. 2005. Quarterly Reports of Disease Management Centre (D.M.C) (2003-2005). Health Ministry, The Government of Islamic Republic of Iran.
14. Jameel S, Zafrullah M, Ahmad M, Kapoor GS, Sehgal S. 1995. A genetic analysis of HIV-1 from Punjab, India reveals the presence of multiple variants. AIDS 9:685-690.
15. Janssens W, Buve A, Nkengasong JN. 1997. The puzzle of HIV-1 subtypes in Africa. AIDS 11:705-712.
16. Joe F. 2004. PHYLIP. Washington: Department of Genome Sciences and the Department of Biology at the University of Washington.
17. Kalish ML, Baldwin A, Raktham S, Wasi C, Luo CC, Schochetman G, Mastro TD, Young N, Vanichseni S, Rubsamen-Waigmann H. 1995. The evolving molecular epidemiology of HIV-1 envelope subtypes in injecting drug users in Bangkok, Thailand: Implications for HIV vaccine trials. AIDS 9:851-857.
18. Kumar S, Tamura K, Jakobsen IB, Nei M. 2001. MEGA2: Molecular evolutionary genetics analysis software. Bioinformatics 17:1244-1245.
19. Kunanusont C, Foy HM, Kreiss JK, Rerks-Ngarm S, Phanuphak P, Raktham S, Pau CP, Young NL. 1995. HIV-1 subtypes and male-to-female transmission in Thailand. Lancet 345:1078-1083.
20. Leitner T. 1997. Genetic subtypes of HIV-1. In: Myers KBG, Foley B, editors. Human retroviruses and AIDS 1996: A compilation and analysis of nucleic acid and amino acid sequences. Los Alamos, New Mexico: Los Alamos National Laboratory. pp (III)28-(III)40.
21. Leitner T, Escanilla D, Marquina S, Wahlberg J, Brostrom C, Hansson HB, Uhlen M, Albert J. 1995. Biological and molecular characterization of subtype D, G, and A/D recombinant HIV-1 transmissions in Sweden. Virology 209:136-146.
22. Louwagie J, McCutchan FE, Peeters M, Brennan TP, Sanders-Buell E, Eddy GA, van Der GG, Fransen K, Gershy-Damet GM, Deleys R. 1993. Phylogenetic analysis of gag genes from 70 international HIV-1 isolates provides evidence for multiple genotypes. AIDS 7:769-780.
23. Louwagie J, Janssens W, Mascola J, Heyndrickx L, Hegerich P, van Der GG, McCutchan FE, Burke DS. 1995. Genetic diversity of the envelope glycoprotein from human immunodeficiency virus type 1 isolates of African origin. J Virol 69:263-271.
24. Mullins JI. 2001. Subtyping HIV-1 by heteroduplex mobility assay. AIDS Research and Reference Reagent Program protocol.
25. Myers GB, Korber Hahn B. 1995. Human retroviruses and AIDS: A compilation and analysis of nucleic acid and amino acid sequences. Los Alamos: Los Alamos National Laboratory.
26. Neilson JR, John GC, Carr JK, Lewis P, Kreiss JK, Jackson S, Nduati RW, Mbori-Ngacha D, Panteleeff DD, Bodrug S, Giachetti C, Bott MA, Richardson BA, Bwayo J, Ndinya-Achola J, Overbaugh J. 1999. Subtypes of human immunodeficiency virus type 1 and disease stage among women in Nairobi, Kenya. J Virol 73:4393-4403.
27. Novitsky VA, Montano MA, Essex M. 1998. Molecular epidemiology of an HIV-1 subtype A subcluster among injection drug users in the Southern Ukraine. AIDS Res Hum Retroviruses 14:1079-1085.
28. Paraskevis D, Magiorkinis E, Magiorkinis G, Anastassopoulou C, Lazanas M, Chrysos G, Vandamme AM, Hatzakis A. 2001. Molecular characterization of a complex, recombinant human immunodeficiency virus type 1 (HIV-1) isolate (A/G/J/K/?): Evidence to support the existence of a novel HIV-1 subtype. J Gen Virol 82:2509-2514.
29. Perelson AS, Neumann AU, Markowitz M, Leonard JM, Ho DD. 1996. HIV-1 dynamics in vivo: Virion clearance rate, infected cell lifespan, and viral generation time. Science 271:1582-1586.
30. Preston BD, Dougherty JP. 1996. Mechanisms of retroviral mutation. Trends Microbiol 4:16-21.
31. Quinones-Mateu ME, Albright JL, Torre V, Reinis M, Vandasova J, Bruckova M, Arts EJ. 1999. Molecular epidemiology of HIV type 1 isolates from the Czech Republic: Identification of an env E subtype case. AIDS Res Hum Retroviruses 15:85-89.
32. Robertson DL, Sharp PM, McCutchan FE, Hahn BH. 1995. Recombination in HIV-1. Nature 374:124-126.
33. Robertson DL, Anderson JP, Bradac JA, Carr JK, Foley B, Funkhouser RK, Gao F, Hahn BH, Kalish ML, Kuiken C, Learn GH, Leitner T, McCutchan F, Osmanov S, Peeters M, Pieniazek D, Salminen M, Sharp PM, Wolinsky S, Korber B. 2000. HIV-1 nomenclature proposal. Science 288:55-56.
34. Rossi P, Moschese V, Broliden PA, Fundaro C, Quinti I, Plebani A, Giaquinto C, Tovo PA, Ljunggren K, Rosen J. 1989. Presence of maternal antibodies to human immunodeficiency virus 1 envelope glycoprotein gp120 epitopes correlates with the uninfected status of children born to seropositive mothers. Proc Natl Acad Sci USA 86:8055-8058.
35. Rubsamen-Waigmann H, von BH, Holmes H, Bjorndal A, Korber B, Esser R, Ranjbar S, Tomlinson P, Galvao-Castro B, Karita E. 1994. Standard conditions of virus isolation reveal biological variability of HIV type 1 in different regions of the world. WHO network for HIV isolation and characterization. AIDS Res Hum Retroviruses 10:1401-1408.
36. Sharp PM, Bailes E, Robertson DL, Gao F, Hahn BH. 1999. Origins and evolution of AIDS viruses. Biol Bull 196:338-342.
37. Smith TF, Srinivasan A, Schochetman G, Marcus M, Myers G. 1988. The phylogenetic history of immunodeficiency viruses. Nature 333:573-575.
38. Soto-Ramirez LE, Renjifo B, McLane MF, Marlink R, O'Hara C, Sutthent R, Wasi C, Vithayasai P, Vithayasai V, Apichartpiyakul C, Auewarakul P, Pena CV, Chui DS, Osathanondh R, Mayer K, Lee TH, Essex M. 1996. HIV-1 Langerhans' cell tropism associated with heterosexual transmission of HIV. Science 271:1291-1293.
39. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680.
40. 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.
41. Triques K, Bourgeois A, Vidal N, Mpoudi-Ngole E, Mulanga-Kabeya C, Nzilambi N, Torimiro N, Saman E, Delaporte E, Peeters M. 2000. Near-full-length genome sequencing of divergent African HIV type 1 subtype F viruses leads to the identification of a new HIV type 1 subtype designated K. AIDS Res Hum Retroviruses 16:139-151.
42. Vanden HM, Decourt JL, De Leys RJ, Vanderborght B, van Der GG, van HH, Saman E. 1994. Genomic cloning and complete sequence analysis of a highly divergent African human immunodeficiency virus isolate. J Virol 68:1586-1596.
43. Wahren B, Ljungberg K, Rollman E, Levi M, Zuber B, Kjerrstrom ZA, Hinkula J, Leandersson AC, Calarota S, Hejdeman B, Bratt G, Sandstrom E. 2002. HIV subtypes and recombination strains-strategies for induction of immune responses in man. Vaccine 20:1988-1993.
44. Wernersson R, Pedersen AG. 2003. RevTrans: Multiple alignment of coding DNA from aligned amino acid sequences. Nucleic Acids Res 31:3537-3539.
45. Zhang L, Huang Y, He T, Cao Y, Ho DD. 1996. HIV-1 subtype and second-receptor use. Nature 383:768.